On 5 July 2018, Fagan was appointed to the coaching staff of Hull City’s Academy. In 2019 Fagan replaced the departing Kevin Maher as under-23 coach at Southend United.

In August 2020, Fagan applied to become the manager of the first team of Southend United. It was later decided by the club that he would not get the role but would continue as the under-23s coach. He later went on to get promoted to assistant manager.

Fagan is currently assistant manager to George Elokobi at National League South team Maidstone United.