In 2006–07, at the start of the season Fletcher retained a place in the first-team but only on the bench and scored in an away win over Charlton Athletic, as well as scoring the headed winner in the away game with Middlesbrough in December and another headed goal in the home win against Charlton in February, making it a double against the club that season. As the season progressed, Alex Ferguson preferred the midfield quartet of Cristiano Ronaldo, Paul Scholes, Michael Carrick and Ryan Giggs, limiting Fletcher to a few substitute appearances. However, with Scholes absent through suspension, he made a starring appearance in United's 7–1 win over Roma in the Champions League quarter-final.