Kilkenny were nursing further wounds after their U21 side was beaten by 50 points in the championship during the week.
The winners had a half-time lead of 6-9 to 0-2 with full-forward Seamus Quigley shooting 2-4.
Sub Ryan Keenan bagged two goals. Declan McCusker shot another, while the impressive Quigley kicked a further eight points.
Scorers for Fermanagh: S Quigley 2-12 (4fs), R Keenan 2-1, J Sherry, B Cox, D McCusker, P Ward (1f) 1-1 each, M Jones 1-0, D Kille 0-3, M Little, N McGovern, R Jones 0-1 each.
Scorers for Kilkenny: S Duggan 0-3fs, G Lawlor 0-1f.
FERMANAGH: C Breen; N McGovern, B Owens, M Jones; D Kelly, S Lyons, B Cox; E Donnelly, J Sherry; M Little, R Jones, E Maguire; D Kille, S Quigley, P Ward.
Subs: N McElroy for Lyons (34), D McCusker for Maguire (36), P Cosgrove for Donnelly (36), R Keenan for Ward (36), M McGrath for Sherry (58).
KILKENNY: D Garvey; R O’Hara, JJ Grace, D Grennan; D Fitzpatrick, M Malone, S Duggan; B Byrne, K Bergin; J Fennelly, R Shore, C Foley; J Dollard, P Donnelly, G Lawlor.
Subs: G Smith for Garvey (36), K O’Brien for Grace (36), J Culleton for Foley (46), B Kehoe for Lawlor (46), P McBride for Fennelly (61).
Referee: M Rock (Clare).