The announcement came after Harbaugh led San Francisco to an 8-8 record and third place finish in the NFC West.
Harbaugh was believed to have a strained relationship with team management.
Speaking on The TK Show podcast with San Jose Mercury News columnist Tim Kawakami on Friday, Harbaugh commented on the nature of his departure from the 49ers.
Kawakami asked if the separation was a mutual decision or if Harbaugh was told that he wouldn't be the coach any more.
"Yes, I was told I wouldn’t be the coach any more," Harbaugh said. "And then that's … you can call it ‘mutual,’ I mean, I wasn’t going to put the 49ers in a position to have a coach that they didn’t want any more. But that’s the truth of it. I didn’t leave the 49ers. I felt like the 49er hierarchy left me."
Over four seasons in San Francisco, Harbaugh led the team to a 44-19 record and three consecutive appearances in the NFC Championship game.