Here is a list of words that you often encounter and which have the exact same pronunciation but are written using different kanji. Often they have different or slightly different meanings, so I have tried my best to describe the difference.
A,I,U,E,O
au
会う Meet
逢う Meet (dramatic, with pathos)
合う Match, fit, suit, agree, be correct, be profitable
遭う Meet, encounter (undesirable nuance)
遇う Meet (by chance) (rare)
aoi
青い Blue
蒼い Pale, blue (skin color)
aku
開く Open (vi)
明く Open (vi) (eyes)
空く Become empty/less crowded
飽く ?
agaru
上がる Enter, rise
挙がる Become prosperous, be captured
揚がる Rise
騰がる Rise (stock prices) (uncommon)
ageru
上げる Give, raise, fly (kite), increase, advance, promote
挙げる Give (example, party), raise
揚げる Fry (in oil), lift
azukaru
預かる Keep in custody, take charge of
与る Participate in
atsui
熱い Hot (thing)
暑い Hot, warm (e.g. weather)
厚い Thick, deep /warm-hearted
篤い Warm, cordial
ayashii
怪しい Suspicious, doubtful
妖しい Strange (beauty), charming
ayamaru
謝る Apologize
誤る Make a mistake
arai
荒い Rough, rude, wild (talk, person, behaviour, temper)
粗い Coarse, rough (skin, texture, net-mask)
itadaku
頂く Receive, take food, be crowned with, wear, live under (a ruler), install (a president), accept
戴く (as above, but uncommon)
iru
居る Be (animate object) (usually written いる)
要る Need
入る Get in, come in
射る Shoot
鋳る Cast, mint (coin)
煎る Fry, parch, broil, roast
utsu
打つ Hit, type
撃つ Hit, attack
討つ Attack, avenge
utsusu
写す Film, duplicate, reproduce, trace, photograph, imitate
映す Project, reflect, cast (shadow)
移す Remove, transfer, infect
遷す Remove, transfer, infect (usually 移す is used)
utsuru
写る Be photographed, be projected
移る Move, be infected
映る Be reflected, harmonise with, come out (on photo)
遷る Move (city) (uncommon)
eru
得る Get (e.g. disease), gain, win (victory), obtain (permission)
獲る Get (animal, game/something hunted)
選る Choose, select
oou
覆う Cover, hide
被う Cover, plate (metal, car, veil)
蔽う Cover, obscur (moon by clouds)
蓋う Cover (with lid), end (fame), make diffuse
okasu
犯す = Commit (crime, rape), violate, rape
侵す = Invade, raid, trespass
冒す = Face, risk (danger), venture
okoru
起こる Occur, happen
興る To rise, flourish
怒る Get angry
osameru
納める Obtain (taxes), reap, supply (goods), lay in (coffin)
収める Obtain (results, profit), pay, accept
治める Govern, manage, subdue
修める Study, complete (a course), cultivate, master, repair
oru
居る Be (animate object) (usually written おる)
織る Weave
折る Fold, break, pick (flower)
kau
買う Buy
飼う Keep/raise (animal)
kaesu
返す Return something
還す Return something (terriroty, runner)
帰す Send back
反す Change, turn over
孵す Hatch (chicken)
kaeru
帰る Go back, go home, return
返る Return, come back (vi)
孵る Hatch (vi)
変える Change (vt), alter, vary, convert, amend
返る Return (vi), come back
換える Exchange, interchange, replace
代える Exchange, interchange, replace
替える Exchange, interchange, replace
kakaru
掛かる Take (time, money) / hang (vi.)
架かる Hang (vi)
kakeru
かける Turn on, dial (phone) / (as suffix) start doing something / lock (with a key)
掛ける To wear, put on / hang (vt) / begin (as suffix) / make a phone-call / cover
multiply / sit down / turn (a switch) / play (a record) / pour (milk, water)
架ける Hang, wear (glasses)
駆ける To run
駈ける Run, gallop
欠ける To lack
翔ける To soar
賭ける To bet, wager
kage
陰 Shade, shadow (usually means shade more than shadow)
影 Shadow, shade (usually means shadow more than shade)
翳 In shadow (something which is hidden from the human eye)
kasu/kasuru
化す/化する Change into, convert into, be reduced, improve (someone)
貸す Lend
課す/課する Impose (tax, duty, homework), charge/assess/levy (tax), give (penalty)
科す/科する Fine (penalty, imprisonment)
掠る（かする) Graze, squeeze, become blurred, exploit
架する Paint (rare)
嫁する Be married
kasuka
微か Faint, dim, small (hope, smell)
幽か Faint, dim, vague (see something)
katai
固い Hard, firm, stubborn (opp ゆるい meaning loose, lenient)
硬い Hard, solid (esp. metal, stone, opp. 軟らかい)
堅い Hard (esp. wood, opp. もろい meaning brittle)
難い Hard, difficult (a task hard to undertake, opp. やすい)
karu
刈る Cut (hair), mow (grass), harvest, trim, reap
駆る Drive (car), spur on, impel
狩る Hunt
借る Borrow, hire
kawaru
変わる Change, be transformed (vi)
代わる Take the place of, relieve, be exchanged (vi)
替わる Take the place of, relieve, be exchanged (vi)
換わる Take the place of, relieve, be exchanged (vi)
kiku
聞く Hear, listen to, ask
聴く Hear, listen to (music, what someone has to say), ask
利く Be effective (medicin, proclamation)
効く Be effective, be useful, help out (your left hand, your nose)
kiru
切る Cut, chop, hash, carve, saw, clip, shear, slice, strip, fell, punch, sever (connections),
pause, break off, turn off, hang up, cross (a street), discount, shake (water) off, finish
着る Wear, put on (from shoulders and down)
斬る Behead, murder
伐る Cut, fell (trees) (usually 切る is used)
kiwameru
極める Carry to extremes
窮める Investigate (e.g. mysteries)
究める Search for, investigate (e.g. the truth, learning)
kumu
組む Put together
汲む Draw water (from well), scoop, pump, have a drink together, sympathise with
酌む Serve (sake)
koumuru
被る Receive (benefit), suffer, sustain (damage, loss)
蒙る Receive, suffer, sustain (uncommon)
sakeru
避ける Avoid
裂ける Split, burst (vi)
saku
咲く Bloom
裂く Tear, split
割く Cut up, separate, spare (time), sever, divide, alienate
sasu
指す Point, put up (umbrella), play
刺す Pierce, stab, prick, thrust, sting, stitch, put (a runner) out,
pole (a boat), catch (with a line), stick
挿す Insert, wear in belt, graft
差す Raise/stretch out (hands), raise (umbrella)
射す Shine (sun), strike (usually 差す is used)
注す Pour/serve (drinks) (usually 差す is used)
鎖す Raise (a gate), open (lock) (usually 差す is used)
点す Light (a fire) (usually 差す is used)
sameru
覚める Wake up
醒める Get sober, come to one's senses
冷める Become cool, abate
褪める Fade, discolour
semeru
責める Blame, critisise, condemn
攻める Attack, assault
suteru
捨てる Throw away, abandon
棄てる Expel, give up, abandon (uncommon)
suberu
滑る Glide, slide, slip
統べる Control, supervise
suru
為る/する Do
刷る Print
摺る Print, draw (e.g. with hand)
掏る Pick someone's pocket
擦る Rub, chafe
摩る Rub, chafe
磨る Polish (usually 磨く(みがく) is used)
擂る Grind, mash, pulverise (not common, usually 擂り潰す is used)
semeru
攻める Assault, threaten
責める Blame
sonaeru
供える Offer, sacrifice, dedicate
備える Furnish, provide for, equip
具える Be furnished with
soru
反る Curve, bend
剃る Shave
taeru
絶える = Become extinct, die out
耐える = Bear, endure, stand (pain, hardships), put up with, take (criticism), tolerate
堪える = Be fit for (duty), equal, bear, endure, put up with (usually 耐える is used)
takuwaeru
貯える Store, lay in stock
蓄える Store away for later use (water, money, provisions)
tatakau
戦う Battle, fight, wage (e.g. war)
闘う Fight (e.g. disease, opposition)
tadasu
正す Correct, adjust, reform
質す Ask, ascertain, verify (if in doubt)
糺す Query (about truth, origin)
糾す Query (uncommon)
tatsu
立つ Stand up, be erected
建つ Stand up, be erected (building)
経つ Lapse, pass
発つ Depart
起つ Rise up, initiate (action)
断つ Sever, cut off (time, path, rope, electiricty), abstain
絶つ Sever, cut off (news, life), abstain
裁つ Cut (cloth)
tameru
貯める Save (in a bank)
溜める Amass, accumulate (e.g. water)
矯める Straighten, correct, cure, falsify
tsukaeru
仕える Serve, work for
支える Be blocked, choke, obstruct (also reads ささえる meaning "support")
tsuku
着く To arrive, reach
付く To adjoin, be attached, (as suffix), be connected with / be dyed, stained
scarred, / start (vi) (e.g. fires) / be added to, accompany, increase
点く To catch fire, (electricity) come on (vi)
突く To thrust, strike, attack, poke
吐く Tell (a lie), breathe
就く Settle in (place), take (seat), study under (teacher)
衝く Pierce, sting (nose, i.e. pungent smell), attack (enenmy) (rare, usually つく is used)
憑く Be possessed (by a demon) (usually つく is used)
搗く Pound (steamed rice into "mochi") (usually つく is used)
附く same as 付く
撞く Strike (bell) (usually 突く is used)
漬く Be soaked in (water) (rare)
tsutomeru
務める Serve, work for
勤める Labour, exert oneself, endeavor
努める Try hard, make an effort, exert oneself
勉める same as 努める (uncommon)
tsumu
積む Pile up, stack
摘む Pluck, pick
詰む Become firm, fixed
抓む same as 摘む (uncommon)
toku
解く Solve, answer, untie
説く Explain, persuade
溶く Dissolve (vt) (e.g. paint)
togu
研ぐ Sharpen, polish
磨ぐ Sharpen, polish, grind, wash rice
砥ぐ ?
totonoeru
整える Put in order (when out of order)
調える Arrange, prepare (limit the amount), raise money
todomaru
留まる Be fixed, stay (in one place)
止まる Be limited to
tonaeru
唱える Recite, chant
称える Assume the name of
tomaru
止まる Stop, halt
泊まる Stay (e.g. in a hotel)
留まる Stay (in a fixed place)
停まる Stop, halt (e.g. train)
toru
取る Take, pick up, harvest, earn, choose
採る Adopt (measure, proposal), pick (fruit), assume (attitude)
撮る Take (photo), make (film)
捕る Capture, catch (fish)
執る Take (trouble), attend (business), command (army)
獲る Gain, get, win
盗る Steal, take
摂る Take (nutrition) (not common, usually 取る is used)
録る Take, record (movie) (not common, usually とる is used)
naosu
直す Repair, correct
治す Cure
naru
成る Become (usually written なる)
鳴る Sound, ring, echo, roar
生る Bear fruit
為る Change, be of use
nioi
匂い Good smell, fragrance, odour, scent
臭い Bad smell, stench odour, scent (also read くさい)
niru
似る Resemble
煮る Boil, cook
noberu
述べる Mention, state, express
延べる Stretch (i.e. make bigger/wider), make (bed)
伸べる Stretch (i.e. make longer)
陳べる State (true feelings) (usually 述べる is used)
noboru
上る Rise, ascend, be promoted
登る Climb
昇る Arise, ascend
noru
乗る Get on, ride in (vehicle), spread (paints), share in, join, be found (in dictionary)
載る Appear (in print), be recorded
hakaru
測る Measure, weigh
計る Measure, weigh
量る Plot, plan, attempt
図る Plot, plan, attempt
謀る Plot, plan, attempt
諮る Consult with, confer
haku
履く Wear, put on (lower body)
吐く Vomit, tell (lie), breathe
掃く Sweep, brush, gather up
刷く Paint (with light brush)
hazukashi(i/meru)
恥ずかしい (adj) Be shy, ashamed, embarrased
辱める Put to shame, ashame (someone)
hanasu
話す Speak
離す Separate (two persons), part, divide
放す Set free (bird), let go of (handle)
haneru
跳ねる Leap, jump, prance
撥ねる Reject, eliminate
刎ねる Decapitate
haru
張る Stretch, spread, pitch, put, stick, paste
貼る Stick, paste
hareru
晴れる Clear up (weather), be sunny
腫れる Swell
hiku
引く Pull, subtract
弾く Play (piano, guitar)
轢く Run somebody over (with vehicle), knock somebody down (usually ひく is used)
挽く Saw (wood), grind (coffee beans, pepper) (usually ひく is used)
惹く Be attracted to, feel drawn to (person, music) (usually 引く is used)
曳く Pull, tow, tug, drag (boat, net), (usually 引く is used)
牽く Pull forward (boat, train) (usually 引く is used)
退く Pull back, retreat (army), step down, resign (usually 引く is used)
hitoshii
等しい Equal, similar
均しい Fair, equal (education, rights)
斉しい Together, the same way (answer, vote etc.)
fukureru
膨れる Swell, expand, get cross/sulky
脹れる (unwanted, unpleasant) Swell (gland), expand, get cross/sulky
fukeru
耽る Indulge, be obsessed with
更ける Be late, advance
老ける To age
蒸ける Become ready to eat after steaming
fuku
噴く Emit, spout
拭く Wipe, dry (e.g. with cloth)
吹く Blow (wind)
葺く Hatch, tile (e.g. roof, not in common use)
fuyasu
増やす Increase, add to (personnel, plants) (general)
殖やす Increase, add to (livestock, savings)
furu
降る Precipitate, fall (rain)
振る Wave, shake, swing, cast (actor)
furuu
震う Shake, tremble, vibrate
奮う Wield (power), show (ability)
振るう Wield (sword), prosper (business)
揮う Exert
篩う Sieve, sift (grains) (usually ふるう is used), screen out (candidate) (usually ふるい落とす is used)
horobosu
滅ぼす Destroy, overthrow (enemy, humanity)
亡ぼす Destroy, overthrow (in gambling, a country)
majiru
交じる Mix with (you can tell the elements apart) (people), associate with
混じる Mix with (you can NOT tell the elements apart) (smell, air), associate with
雑じる Mix with (as above) (foreign substance)
matsuru
祭る Deify, enshrine
祀る Deify, enshrine (person, great man)
奉る Offer, present
纏る ?
miru
見る See, watch
観る View (flowers, movie)
診る Examine
看る Look after, take care of
moukeru
設ける Create, establish
儲ける Earn, gain, be profitable, bear (a child)
moru/moreru
盛る Prosper, flourish, copulate
漏る/漏れる Leak, run out
洩る/洩れる Leak out (information (usually 漏れる is used)
yameru
止める Stop, cease, put to an end
辞める Retire
yawarakai
柔らかい Soft, tender, flexible (elastic, e.g. a pillow, opp. 堅い, 固い)
軟らかい Soft, weak (with no resistance, e.g. ripe fruit, opp. 硬い)
wakaru
分かる Understand (circumstances, story) (usually わかる is used)
判る Understand, know (difference, good and evil)
解る Understand (language, meaning) (usually わかる is used)
waku
湧く Grow hot (temperature), gush forth (water, insects)
涌く Grow hot (temperature), gush forth (water, insects)
沸く Boil (water), get excited (cheer)
wataru
渡る Cross over, go across
渉る Extend
亘る Go beyond, extend (boundary, time)
亙る Go beyond, extend (uncommon)