James O'Connor, who guided Fr O'Neill's to the Cork Premier Intermediate title in 2019, will take over the All-Ireland Club champions.
The Waterford man led the East Cork club all the way to the All-Ireland Intermediate final in Croke Park last month, where they were pipped by Kilkenny's Tullaroan in a 3-19 to 5-12 thriller.
He famously coached rank outsiders Carrigtwohill to the Cork senior title in 2011.
Kilkenny legend Henry Shefflin stepped down as Ballyhale boss after the Kilkenny kingpins claimed their second senior All-Ireland in a row last month, defeating Borris-Ileigh at Croke Park.
And while O'Connor will now miss out on a first-ever senior campaign for Fr O'Neill's, he takes the reins as Ballyhale go in search of an All-Ireland hat-trick.
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