Fans from the Merseyside area are likely to be stuck in the capital due to the late 5.15pm kickoff time, which means that groups of spectators will miss the last train back up to Liverpool.
A spokesman for the Merseyside branch of the Liverpool FC Official Supporters Club told The Metro: "The final should kick off at 3pm and everything else should work around that fixture.
"The last people who are thought of by the FA are the fans. We are seen as a money-making machine who will do anything to follow their clubs."
The scheduling was decided by the Football Association due to a full Premier League program on the same day.
The impending engineering works were planned out by the Network Rail 18 months ago.