In January 2005, Fanning succeeded Jim Greene as manager of the Mount Sion senior hurling team.
[3] On 9 November 2009, Fanning joined the Waterford senior hurling management team as a selector under Davy Fitzgerald.
[5] In September 2011, Fanning declined to put his name forward for the vacant managers' position after the resignation of Fitzgerald.
[6] In November 2016, Fanning joined the Wexford senior hurling management team under Davy Fitzgerald as a selector.
[9][10] On 17 September 2018, Fanning was appointed to succeed Derek McGrath as manager of the Waterford senior hurling team.