Gregan left Leeds on 5 January 2007 after reaching an agreement over the remainder of his contract, and signed a two-and-a-half-year contract at Oldham three days later. His performance in their 3–0 win away to Walsall on 22 September 2007 earned him a place in the League One Team of the Week.
Gregan returned to Darlington on 4 June 2012 as a player-coach, as part of new manager Martin Gray's backroom staff. He was appointed as joint manager of Darlington, alongside Brian Atkinson, on 1 October 2017 for the rest of the 2017–18 season after Gray left for the club's National League North rivals York City. However, the two left the club four days later without having taken charge of a match. With Atkinson also being a director of the Martin Gray Football Academy (MGFA), Football Association rules meant he was unable to hold the Darlington managerial position as the academy's owner was in charge at another club. Gregan turned down the offer of a six-month contract to take over as manager on his own, as he would have had to relinquish his own role the MGFA.
Gregan joined Gray at York in December 2017 as a part-time defensive coach. He took up the full-time position of assistant manager in July 2018 but left the club on 19 August along with Gray.
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