French side Nancy had taken an early lead at the KC Stadium, but Fagan levelled in the second half with a header from Darryl Duffy's cross.
City line-up: Boaz Myhill; Mark Lynch, Alton Thelwell, Michael Turner, Andy Dawson; Craig Fagan, Keith Andrews (John Welsh, 45), Dean Marney, Stuart Elliott; Darry Duffy (Nick Barmby, 58), Billy Paynter (Ben Burgess, 58).
Un-used subs: Tom Woodhead, Michael Byron, Tom Matthews, Russell Fry, Stuart Green.