It has been revealed that some United fans have been able to purchase tickets equivalent to those on offer to away supporters £5 cheaper.
As is common practice for Cup games, the clubs had agreed a standard price for home and away fans, in this case £45. But United members have been able to buy them at a discounted rate of £40.
United claim this is an offer available only to members under a long-standing scheme - one that was also operated for the third-round replay against West Ham last week - but Fulham claim they were not informed of the discount.
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."
Fulham made their complaint public via their official Twitter account.
"Fulham Football Club has contacted The FA to complain about Man United discounting FA Cup match tickets for their fans," read the tweet.
The FA has received the complaint and is understood to have written to United for a formal explanation.