Parfitt, who also oversees BBC 1Xtra and the Asian Network, will leave at the end of July to pursue new opportunities.
The BBC said that Parfitt, who has been in the job since 1998, had helped bring record audiences to Radio 1 and 1Xtra.
His 13 years in the role make him the longest-serving controller Radio 1 has had since its launch in 1967.
"I am immensely proud to have held this position and I leave with all three stations in great shape, with their listening figures at record highs and following a great BBC-wide Glastonbury event," Parfitt said.
"I'm most proud of the incredible teams I'm leaving behind - a group of talented, hard-working, creative and inspirational people who are a credit to the BBC."
