In his final season at Preston, he was loaned out to Gillingham and then back to Stevenage before being released and joining Burton Albion in June 2014.

Whilst playing, Mousinho was elected as chairman of the PFA in May 2021, a position he held until January 2023, leaving in order to take on his first managerial role, as head coach of League One club Portsmouth, where he led the team to promotion to the EFL Championship as champions of EFL League One in the 2023–24 season.

[5] Mousinho was signed by Brentford manager Martin Allen during the 2005–06 season, after returning from the United States where he was studying and playing football at the University of Notre Dame.

[8] Mousinho made his Football League debut for the club two months later in a 4–1 away win over Tranmere Rovers on 17 December 2005, coming on as a 76th-minute substitute.

Initially he acted as cover for regular right-back Kevin O'Connor, but was then played in a central midfield role.

[8] At the end of the 2007–08 season, Mousinho was transfer-listed by manager Andy Scott because he did not feature in the club's future plans and, as a result, his first-team chances would be limited.

[38][39] Mousinho returned to the first team for the 2011 play-off final against Torquay United at Old Trafford on 28 May 2011, a game in which he scored the only goal with a strike from 20 yards in a 1–0 Stevenage victory.

[42] He returned to the first team on 16 August 2011, starting in a 3–1 away victory against AFC Bournemouth, scoring Stevenage's second goal of the game from the penalty spot.

[43] Mousinho's second goal of the season came in Stevenage's 5–1 win against Sheffield Wednesday at Broadhall Way, beating defender Rob Jones for pace before driving a shot from 20 yards past goalkeeper Richard O'Donnell.

[44][45] He injured a metatarsal bone in his right foot in Stevenage's 1–0 away victory against Hartlepool United in the FA Cup on 12 November 2011, and was subsequently ruled out of first-team action for six weeks.

[48] Three days after their play-off semi-final defeat, on 17 May 2012, Mousinho turned down an improved contract and opted to leave the club after two years.

[57] Mousinho made his Gillingham debut a day after signing, playing in a 1–1 home draw with Brackley Town in the FA Cup.

[59] Mousinho suffered a hamstring injury in a 4–1 defeat to Rotherham United four days later, and returned to his parent club before the end of the loan agreement.

[64] Following his release from Preston, Mousinho joined League Two club Burton Albion on a two-year deal on 6 June 2014.

[76] He left Burton by mutual consent on 31 August 2017, signing a two-year deal with Oxford United on the same day.

[75] Burton manager Nigel Clough stated he had advised Mousinho "that if he had the opportunity to get a longer contract with a club which was also further south and that was the best thing for him then we wouldn't stand in his way.

[83] He signed a new one-year contract on 30 June 2020, which enabled him to play in Oxford's League One play-off matches, the club having finished in fourth place, determined on an unweighted points-per-game basis.

[87] The injury ultimately ruled him out for six weeks, during which he was a part of Oxford manager Karl Robinson's first-team coaching staff.

[88][89] He suffered a recurrence of the knee injury in Oxford's 4–0 home victory against Northampton Town on 15 December 2020 and underwent surgery in January 2021, which meant he missed the remainder of the 2020–21 season.

[89][90] Having returned to pre-season training at Oxford, Mousinho signed a new two-year contract on 5 July 2021, taking on a player-coach role.

[90][91] Having made 151 appearances for Oxford over four seasons, Mousinho left the club in order to take up the role of head coach at Portsmouth.

[92] Portsmouth chief executive Andrew Cullen stated Mousinho's leadership and motivational skills were an important reason behind his appointment.

[96] He won the award for a second time in February 2024, four wins from an unbeaten five matches further cementing their place at the top of the league.

[103] He made the transition from central midfield to centre-back during his time at Burton Albion and spent the 2016–17 season playing in both roles.

[77][91][104] Mousinho was elected as chairman of the newly formed Professional Footballers' Association (PFA) players' board in May 2021.