'Tomorrow Never Knows' - from the band's 1966 studio album Revolver - was featured in the episode 'Lady Lazarus'.
The overall licensing cost for the track was $25,000 (£15,480), according to The Wall Street Journal.
While Lionsgate - the studio that produces Mad Men for AMC - refused to confirm the amount, a spokesperson did reveal that the deal was the most expensive of its type to date.
The appearance of 'Tomorrow Never Knows' also marks the first time a master recording by the Beatles has been licensed for a television show, it was claimed.
In February, it was reported that Sir Paul McCartney had signed a deal allowing his music to feature in Mad Men.
The music legend was also rumoured to be in line for a cameo appearance, but series star Jon Hamm (Don Draper) later dismissed the suggestion.
"We've always shied away from anybody that is terrifically recognisable on the show," he explained. "The man is legendary and deservedly so. But I think that rumour should be taken with a certain degree of salt."
Mad Men continues on Sky Atlantic on Tuesday nights at 9pm. It airs in the US on Sundays on AMC.
Watch a promo for the 'Lady Lazarus' episode below: