This report does not cover payments made by Premier League clubs.
United's £5,000 of fees was accrued over deals involving 22 different players.
The big spenders were in the Championship, with the second tier of English football accounting for 88 per cent of the outlay on agents.
Southampton paid the most - £842,533, followed by Sunderland, Stoke and Birmingham.
In League One five clubs paid out nothing to agents during this period.
"We understood the culture of paying agents would take time to reverse, these figures underline that reality," said Football League chairman Sir Brian Mawinney.
"New regulations, introduced this summer, have helped bring greater levels of transparenct and integrity to the transfer system."