In the 2009–10 season, Murphy continued as Connacht's first choice scrum-half. He played in 14 of Connacht's 18 games in the 2009–10 Celtic League, starting all but two of these. At European level, Murphy played in all of Connacht's 2009–10 Challenge Cup games as they reached the semi-final, being beaten 19–12 at the Sportsgrounds by Toulon. In the following season, Murphy played in 21 of Connacht's games under new coach Eric Elwood in the 2010–11 Celtic League, which had been expanded to 12 teams. Murphy played in all six of Connacht's games in the 2010–11 Challenge Cup, starting five of them, as Connacht failed to make it past the pool stage. Over the course of these seasons, Murphy would, on occasion, serve as captain of Connacht.