King K Rool poses from his Donkey Kong 64 cover.

K. Rool, having become more unstable from the previous defeats, returns in the game Donkey Kong 64 for the Nintendo 64, where he randomly appears one day on a Mobile Island Fortress. K. Rool had planned to blow up Donkey Kong Island with a powerful megaweapon called the Blast-O-Matic. Fortunately, the mobile fortress ends up crashing because of the usual incompetence of the Kremling drivers. In an attempt to distract Donkey Kong while the Blast-O-Matic gets prepared to shoot, K. Rool has several of his Kong friends imprisoned. These are: Diddy Kong, Tiny Kong, Lanky Kong and Chunky Kong. He also steals Donkey Kong's Golden Banana Hoard.

K. Rool, along with his unnamed pet Klaptrap, appear in several of the game's cutscenes, watching the Kongs progress and chastising his own minions' (the bosses of the game) failures. A notable scene shows K. Rool demand that nobody leaves the Blast-O-Matic until it is repaired.

Eventually, K. Rool's henchmen succeed in repairing the Blast-O-Matic, just as the Kongs enter Hideout Helm. K. Rool demands that the weapon be fired right away, despite the warnings that it is not fully tested and it could possibly explode, killing them. After the Kongs permanently shut down K. Rool's mechanical island and the Blast-O-Matic laser weapon, K. Rool tries to escape in an airship, the King Kruiser II. Unfortunately for K. Rool, the airship ends up being knocked to the ground and destroyed by a freed K. Lumsy, his gigantic younger brother. Venturing inside the crashed vessel, the five Kongs found a boxing arena filled with spectators and K. Rool, as his boxer alias King Krusha K. Rool, ready for the final battle. K. Rool will create multiple shockwaves by slamming the ground, throw his gloves as a boomerang, and uppercut the Kongs after charging at them. Engaging K. Rool in a bizarre series of battles – which include blasting out of barrels into K. Rool's face, dropping spot-lights on K. Rool, making him slip on banana peels, shrinking down and blasting his toes and (generally) pummeling him – the Kongs manage to claim victory.