Mousinho joined the Blues from Oxford United, where he had a player-coach role, in January 2023, steering them from 15th to eighth in League One by the end of the season.
Portsmouth secured promotion and the League One title in a memorable 3-2 victory over Barnsley in April that saw fans flood onto the pitch after the full time whistle.
Mousinho brought second-tier football back to Portsmouth for the first time in 12 years.
“I have loved every minute of my time at Pompey so far and am delighted to have agreed an extension to my contract,” Mousinho said.
“I am grateful to Michael and the board for the faith they have shown in me, the coaching team and players, as well as for the support we continue to receive from our magnificent supporters.
“Winning the League One title last season is, of course, the highlight and now our full focus is on establishing this side in the Championship.”
The Eisners were at Fratton Park last Sunday – the first time they have flown over from the US for a match this season – to rubber-stamp the new deals for Mousinho and Hughes.