On 9 November 2009, Fanning joined the Waterford senior hurling management team as a selector under Davy Fitzgerald.[4] In his first season in the role, he helped guide Waterford to a Munster final defeat of Cork after a replay.[5] In September 2011, Fanning declined to put his name forward for the vacant managers' position after the resignation of Fitzgerald.[6]
Wexford
In November 2016, Fanning joined the Wexford senior hurling management team under Davy Fitzgerald as a selector.[7] During his first year as a selector, Fanning helped secure promotion to Division 1A of the National Hurling League.[8] Later that season he helped guide Wexford to their first Leinster Championship defeat of Kilkenny since 2004 as well as a first Leinster final appearance since 2008.[9][10]
Waterford
On 17 September 2018, Fanning was appointed to succeed Derek McGrath as manager of the Waterford senior hurling team.[11][12] He was joined on the management team by James Murray and Patrick Kearney who acted as selectors. On 2 August 2019, it was announced that Fanning would be stepping down as Waterford manager after one year in charge.