He was appointed manager of League One club Milton Keynes Dons on 10 May 2010, having previously been the club's assistant manager under previous boss Paul Ince. At 29 years of age, he was the youngest manager at the time in the Football League and former England coach John Gorman was named his number two. In the 2010–11 season, his first season in charge, Robinson guided MK Dons to fifth place in League One. This was regarded as a good achievement, improving on the Dons' points total over the previous season. The team lost in the playoffs to Peterborough United over two legs. In the 2011–12 season, he continued making impressive strides, attracting big name players and guiding his side to another 5th-place finish and was again in the play-offs. During the season, he signed a 3-year contract extension with the Dons. Robinson masterminded arguably MK Dons greatest victory, a 4–0 EFL Cup win over Manchester United on 26 August 2014, as well as leading the Dons to promotion to the Championshipfor the first time, finishing as runners-up in League One. On 20 July 2015, Robinson signed a contract extension at the Dons along with the club's Head of Coaching, Richie Barker. However, MK Dons did not publicise the length of either deals. Robinson's MK Dons suffered relegation from The Championship during the 2015–16 season, with MK Dons finishing in 23rd position. On 23 May 2016, it was revealed that Robinson had turned down an offer from Massimo Cellino to become Leeds United's Head Coach. On 23 October 2016, MK Dons released a statement saying that Robinson had been relieved of his duties following the 3–0 defeat to Southend United the previous day which took the club's winless run to four games.
Robinson was named the new Charlton Athletic manager on 24 November 2016 following the sacking of Russell Slade, taking full charge of the club from Monday 28 November 2016. He departed by mutual consent on 22 March 2018.
Oxford United
On 22 March 2018, Robinson was appointed as the new head coach of League One club Oxford United, joining on the same day as his departure from Charlton Athletic. He signed a two-and-a-half-year contract with the club, extended to 2022 in August 2019. In December 2019, Robinson was charged by the Football Association for using abusive language to a match official.