The significant move, coupled with the repayment of external monies owed, means the west London club no longer has any outstanding debts.
The development has come to light with the announcement of Fulham's financial report for the 2011/12 season, which saw the club report an operating profit of £1.2million and revenue figures of £79.3million.
The club has enjoyed an increase in attendance of 0.6%, which saw overall occupancy at Craven Cottage rise to 98.4% for the season.
With plans afoot to increase the stadium's capacity to 30,000 by developing the Riverside Stand, Al Fayed believes the club's future is bright.
"Fulham continues to make great strides and, following planning permission for the redevelopment of the Riverside Stand, we will continue to prosper and grow," he said in a statement released to Press Association Sport.
"For almost the last 15 years, I have ensured the club moves in the right direction and remains true to our proud history, strong heritage and past traditions."