The London club have complained to the Football Association after discovering that some United fans have been able to purchase seats equivalent to those on offer to Fulham supporters £5 cheaper.
As is common practice for FA Cup games, the clubs had agreed a standard price of £45 for home and away fans but United members have been able to purchase them at a discounted rate of £40. United say that is an offer available only to members under a long-standing scheme and it should not have come as a surprise.
Fulham claim they were not informed of the discount and it is understood they would not have agreed to it had they known.
A United spokesman said: "Fulham fans are paying the same as United fans who are not members. A discount scheme has existed for members for around 20 years. We're surprised it has come as a surprise to them."
United most recently operated the scheme for their third-round replay against West Ham last week.
Fulham made public their complaint via their Twitter account.
A tweet read: "Fulham Football Club has contacted The FA to complain about Man United discounting FA Cup match tickets for their fans."
The club have made no further comment but are understood to feel they should have been informed beforehand. They fear their fans will be put off from travelling.
The FA has received the complaint and is understood to have written to United for a formal explanation. Fulham themselves have set a price of £49 for adult away fans when they host United in the Barclays Premier League on February 2.