After leaving Drogheda, Keegan signed for Bohemians in January 2009 and slotted seamlessly into his favourite position of central midfield. His status at the club rapidly grew to such an extent that he captained the side when Owen Heary was absent. He claimed his first silverware for Bohs in the 2008/2009 season when they won the League of Ireland Cup, beating Waterford United 3–1 at the RSC. The success didn't end there though as Bohs subsequently won the first back-to-back titles in their 119-year history. During the 2010 season, Keegan was named captain for a League of Ireland XI that would play Manchester United in a friendly match at the newly opened Aviva Stadium. He was also named PFAI Chairman in November 2010 replacing Stephen Rice in the position. At the end of the 2010 season, with his future at Bohs in doubt due to financial difficulties at the club, he spent time on trial at Reading and Doncaster Rovers.
Doncaster Rovers
After impressing on trial at Doncaster, Keegan signed for the club on 17 January 2011. In May 2012, Keegan was released by the club after the expiry of his contract. However, in an about turn by the club, on 17 July 2012, Keegan signed a new one-year deal with the South Yorkshire club. Following a successful season, and playing in pre-season friendlies, he signed another one-year deal on 25 July 2013. Keegan had a solid beginning to the season with 13 consecutive starts in League games after missing the first match, and then he picked up a hamstring injury preventing him training until January.
In July 2017 Keegan signed for the League of IrelandFirst Division league leaders Waterford. Just one day after signing Keegan scored his first goal for the club and it proved to be a crucial one as Waterford beat Longford Town 1–0 which kept them in the driving seat for the title. After Waterford beat Wexford 3–0 and Cobh Ramblers were defeated 3–0 by Cabinteely Waterford were officially crowned league champions and promoted back to the League of Ireland Premier Division. Keegan finished the season with 10 appearances and 1 goal to his name as Waterford won promotion. Just after Waterford had won the league Keegan confirmed he would stay on at Waterford for the 2018 season as they returned to the League of Ireland Premier Divisionfor the first time in ten years. It was confirmed one week before the 2018 season that Keegan was appointed the new captain of Waterford.
Bray Wanderers
In December 2018 Keegan signed for First Division side Bray Wanderers. Keegan made his debut for Bray in their opening match of the 2019 season away to Cabinteely. A week later he scored his first goal for Bray in a 2–0 home win over Limerick. Keegan finished his first season with Bray with 26 appearances, scoring 3 goals. In November 2019 Paul signed a new contract to keep him at Bray until the end of the 2020 season.
