When Link opens the Boss door, he will enter a room with a few pots and a large hole in the floor. When Link falls down the hole, he will enter the combat area. A room with nothing but a square pit of lava in the center. Gleerok will slowly rise up from the lava and roar.
The battle will begin with Gleerok shooting fire balls at Link. Link can dodge these fire balls and circle around Gleerok. When Link has a clear shot, he can use the Cane of Pacci to flip his back shell over. The shell will land on him and break while he will fall down, stunned. Link can run up Gleerok's neck to the small crystal on his back and slash it furiously at it. Eventually, Link won't be able to hit the crystal anymore. When this happens, Link can run back up his neck to the main land. He will ease into the lava and blocks will fall from the ceiling. If Link did enough damage, the lava in the center of the room will rise up, leaving only one strip of safe land around the room. The lava will fall back down eventually, and Gleerok will come back up.
Gleerok will shoot a continuous wave of fire on one side of the arena, so Link has to stay away from there to be fine. In this round, Gleerok will move around a little bit faster and shoot fire balls a little more often. Link can just move around him again and shoot his back with the Cane of Pacci. He will fall down again, so Link can run up his neck and slash the crystal again. Link must run off his back before he sinks in to the lava. The blocks will fall again and the lava will rise again, so Link must avoid it as normal. Gleerok will rise out of the lava again.
This time around, Gleerok will shoot continuous flames at two sides, so Link must be watchful. He will also spin around a lot faster. Otherwise, the fight is the same. Link can flip his shell and slash his back crystal. After he has taken enough hits, the screen will go white and Link and Gleerok will appear at the bottom part of the arena. Gleerok will start exploding and eventually blow up into a cartoony puff.
The lava will harden and Link will walk into the center of the room. The Fire Element will float down to Link's hands. A Heart Container and a warp tile will appear at the top of the room. Link can grab the Heart Container and head through the warp tile to go back to the entrance of the dungeon.