There were reports earlier on Thursday that Barker had been dismissed and the club have now made the news official on their website.
"Richie Barker has left his position as Portsmouth Football Club manager by mutual consent," a statement said. "Following a meeting between Richie and the board, both parties agreed that it was in the best interests of the club.
"Portsmouth Football Club would like to thank Richie for all his work and wish him well for the future."
The club also confirmed that Andy Awford would take over as caretaker manager until the end of the season.