Baldini became director of football at Roma in 1999, where he remained until his resignation in March 2005. He joined Fabio Capello at Real Madrid in 2006, and when Capello took over as the England manager in December 2007, Baldini became assistant manager. His role at the national team of England involved scouting, managing the supporting staff and generally making the job as easy as possible for Capello. He left England after their successful UEFA Euro 2012 qualification and joined Roma before the start of 2012, but was assisting the team well before then. Since then, former Roma manager Luis Enrique, Director Walter Sabatini and himself have undergone a major revolution at the club alongside new owner Thomas R. DiBenedetto to try and instill a system of running a football club similar to that of Barcelona. However, his time at Roma was criticised by removing Luis Enrique as manager and replacing him with Zdeněk Zeman, which Baldini believes appointing Zemen was a mistake and said the club wanted to give the fans a spectacle. Baldini left his post at Roma by mutual consent on 5 June 2013. On 19 June 2013, Baldini was confirmed in the role of technical director of Tottenham Hotspur.
Tottenham Hotspur
At the end of the 2012–13 Premier League season, then-Tottenham manager André Villas-Boas openly pushed for someone to be employed as a technical director, "someone who has experience of dressing rooms, represents the club, and is able to link up with players and agents." Soon after, on 19 June 2013, Baldini was appointed to the role. He immediately oversaw the departures of Spurs players Steven Caulker, Tom Huddlestone, Clint Dempsey, Scott Parker and Gareth Bale, the latter for a reported world record fee of £85.3 million to Real Madrid. Baldini was also thought to be responsible for signing several replacement players during the same summer, including Paulinho, Nacer Chadli, Étienne Capoue, Roberto Soldado, Vlad Chiricheș, Christian Eriksen and Erik Lamela. Later in 2013, however, Villas-Boas was sacked by the Tottenham Board on 16 December following a humbling 5–0 home defeat to Liverpool. It is thought that Baldini offered his resignation, perhaps as a sign of accepting culpability for the poor form of the team. It was widely discussed in the media at the time that most of the players signed by Baldini were not performing as well as had been expected. Baldini, however, remained in his post after new manager Tim Sherwood replaced Villas-Boas. Baldini left his role as technical director on 28 September 2015 to spend time outside football.