Naka starts his career at Sega, initially working on programming various games. Details of his specific early projects are not always widely publicized, but he gained valuable experience in game development.

Naka contributes to the development of several Sega arcade games, honing his skills in programming and game design within the competitive arcade environment. One notable title is 'Girl's Garden' on SG-1000.

Yuji Naka, along with Naoto Oshima (character design) and Hirokazu Yasuhara (level design), creates 'Sonic the Hedgehog' for the Sega Genesis/Mega Drive. The game is a massive success, establishing Sonic as Sega's new mascot and rival to Nintendo's Mario.

The sequel to Sonic the Hedgehog is released, introducing Tails, Sonic's sidekick. The game further solidifies the franchise's popularity and establishes Naka as a key figure in the industry.

Naka and his team continue to develop numerous Sonic games throughout the 1990s, including 'Sonic 3 & Knuckles', 'Sonic CD', and 'Sonic Adventure'. These games push the boundaries of console technology and expand the Sonic universe.

Naka leads the development of 'Sonic Adventure' for the Sega Dreamcast, marking Sonic's transition to 3D gaming. The game is a critical and commercial success, showcasing the Dreamcast's capabilities.

Naka continues to produce and direct various Sonic titles, although his role becomes less hands-on as the team expands.