Naka started as an employee for Sega, and was the head of Sonic Team. His debut game for Sega was called "Girl's Garden" and was released for the SG-1000 in 1984. Among his most recognizable games would be Sonic the Hedgehog, where along with creator Naoto Ōshima, established a new mascot and killer-app for the Sega Genesis making the system a giant opponent against Nintendo and Mario. He has made many Sonic games and other notable titles like NiGHTS into Dreams, Burning Rangers, and Phantasy Star Online. Though he had many conflicts with Sega in the past, like the Sonic Xtreme conflict, Naka enjoyed his job. The final game he made for Sega was Shadow the Hedgehog.
By 2006, Naka had grown tired of "mak[ing] Sonic games", so he decided to leave Sega. Naka started his own company called PROPE. Naka has proposed that it is healthier for the game industry to experiment and create new IPs, rather than recycle old ones. This, overall, and not merely his own work on Sonic games, has fueled him to develop independently.
During a Quick Look of then-current Game Room releases, Jeff and Ryan went off the rails and delivered a Quick Look of the XBLA re-release of Sonic Adventure for the Dreamcast. During that portion of the video Ryan stated that Big the Cat was his favorite member of the Sonic Team. Jeff in response stated "I'm more of a Yuji Naka guy myself."