Below you can see where you can find the golden skulltulas:
You will receive a reward after you have killed a certain number of Skulltulas and collected their Tokens. You will receive your prize at the spider house in Kakariko Village.
10 Tokens: Adult's Wallet (where you can store 200 rupees)
20 Tokens: Stone of Agony (your
rumble pack will vibrate when you are close to a secret)
30 Tokens: Giant's Wallet (where you can store 500 rupees)
40 Tokens: Ten Bombchus
50 Tokens: Piece of Heart
100 Tokens: Golden Rupee
Skulltulas usually avoid sunlight. So, especially go out at night. You will find that you need to use your Boomerang or Longshot to collect some Tokens. You can keep bugs in a bottle and throw them in a Soft Soil for a Golden Skulltula. In the temples, you can figure out whether you need to be a child or an adult, and day or night doesn't matter.
KOKIRI FOREST (3):
Young Link/Night Behind the house of the know-it-all brothers
Adult Link/Night Behind the house of the twins
Young Link Plant some bugs in the ground next to the shop
Hyrule Field (2):
Both/Always Near the gate to Hyrule Castle
Both/Always Place a bomb in the middle of the stone circle near Gerudo's Fortress
Hyrule Castle (4)
Young Link/Always Play the Song of Storms near the castle entrance to open a cave
Adult Link/Always After Ganon takes over the castle, near the bridge/gate
Lon Lon Ranch (4)
Young Link/Always In a tree at the entrance
Young Link/Night Behind the barn
Young Link/Night In a corner northwest of the barn
Young Link/Night Second window in Talon's house
Kakariko Village (6)
Young Link/Night A kid in the graveyard is kept awake by the rustling of a skulltula
Adult Link/Night On the roof of Impa's house
Lost Woods (3)
Young Link/Always Throw a bean in a Soft Soil near Skull Kid
Adult Link/Night Plant a bean as a child and ride the plant as an adult. The plant leads to a golden skulltula
Young Link/Always Soft Soil near the shortcut to Zora's Domain
Death Mountain (4)
Adult Link/Night Small platform above the entrance of Dodongo's Cavern
Adult/Night At the end of the falling rocks
Young Link/Always Soft Soil in front of the entrance of Dodongo's Cavern
Goron City (2)
Young Link/Always Hidden in a crate at the highest level
Adult Link/Night On the platform high in the middle
Zora's River (4)
Young Link/Night In the shadow of the ladder
Young Link/Always In a tree at the mouth of the river
Adult Link/Night At the middle of the river
Adult Link/Night On the wall near Zora's Domain
Zora's Domain (1)
Adult Link/Night At the top of the waterfall when it's frozen
Zora's Fountain (3)
Young Link/Always In a tree in the southeast
Young Link/Night To the right of the tree stump
Adult Link/Night In a secret cave next to the Fairy's Fountain
Lake Hylia (5)
Adult Link/Always In a chest at the bottom of the pool in the Laboratory
Young Link/Night Behind the Laboratory
Adult Link/Night In a dead tree above the entrance to the Water Temple
Young Link/Always Throw some bugs in the Soft Soil near the Laboratory
Graveyard (2)
Young Link/Night Along the outer walls
Young Link/Always Soft Soil
Sacred Meadow (1)
Adult Link/Night In the east of the stairs
Death Mountain Crater (2)
Young Link/Always Soft Soil at the crater
Young Link/Always In a crate at the entrance
Gerudo Valley (4)
Young Link/Night On the dirty wall near the bridge at the beginning
Adult Link/Night Guards are kept awake by a skulltula
Adult Link/Night Under the big rock
Young Link/Always Soft Soil
Gerudo Fortress (2)
Adult Link/Night On the wall of the building in the east
Adult Link/Night At the horseback archery game behind a target pole in the north
Haunted Wasteland (1)
Adult Link/Always In the stone building
Desert Colossus (3)
Adult Link/Night In the palm trees
Adult Link/Night Ride the plant you planted as a child
Young Link/Always Soft Soil
Fire Temple (5)
1. The first time you encounter flying tiles, next to the Like Like on the wall
2. In the room with the stones, you suddenly hear rustling in a corner, bomb the wall
3. On a climbing fence leading to the 5th floor
4. On the 5th floor on the wall next to the entrance
5. The second time you encounter flying tiles, next to the Like Like on the wall
Ice Cavern (3)
1. On the left by the icicles on the ground in the room with the spinning thing
2. In the room with the blue fire, on the ceiling
3. On the left wall near a door
Water Temple (5)
1. You need your Longshot for this. On the right wall in the room with the waterfall and moving platforms
2. In the river with the whirlpools, somewhere on the wall
3. In the pillar in the middle, on the ceiling
4. In a river with rolling stones behind the waterfall
5. When the water is at its lowest level, go to the first floor in the room in the south. Sink down with your Iron Boots and break the fence with a Spin Attack
Shadow Temple (5)
1. When you are in the room with the spinning blades, enter another room
2. After pushing the big stone under the falling spikes, climb on it and there is a skulltula in a cage on the right
3. Bomb the big skull and kill the skulltula
4. Across from the ladder leading to the boat, summon the scarecrow and hookshot to it
5. Behind the three spinning giant skulls
Spirit Temple Child (3)
1. On the climbing fence that opens after you have collected all the rupees
2. By the stone steps leading from the 1st to the 2nd floor
3. In the hallway before you fight the Iron Knuckles behind you
Spirit Temple Adult (2)
1. In the room with the rolling stones, play your Song of Time the first time and look where the block was originally
2. To the left of the large statue. Summon the scarecrow and hookshot to it