Jose Mourinho's side raked in £37million, £15m less than Tottenham despite exiting at the same stage of the competition as the north London side.
The reason behind the difference in revenue is due to United sealing their spot in the 2017-18 Champions League by winning last season's Europa League.
Semi-finalists Liverpool have earned £57m, the most out of the five English teams involved in this year's instalment, with that figure set to rise even further.
If Liverpool beat Roma in the upcoming semi-final and win the final in Kiev they could be set for a £71.7m Champions League windfall.
Of the other three Premier League sides who took part in this year's competition, Chelsea earned £55m, Manchester City £54m and Tottenham £52m.
The five English clubs' revenue comes in part from them dividing up BT Sport's £119m deal to broadcast the Champions League.
A similar deal in Italy means Roma would receive more should they win the competition because only three Serie A sides — Roma, Napoli and Juventus — were involved this season.
The other semi-finalists, Real Madrid and Bayern Munich, would make £75m each should they go all the way and win the Kiev final.
The manner in which fees are determined is also dependent on group stage results and whether or not clubs qualified through the Champions League play-offs.
United were dumped out of Europe's premier club competition by Sevilla in the last-16 with Wissam Ben Yedder's brace securing a shock win for the Spaniards at Old Trafford.
Chelsea lost to Barcelona in the last-16, Tottenham fell to Juventus at the same stage and Liverpool overcame City in the quarter-finals.