The Glovers took an early lead but found themselves 5-1 down at the break before eventually falling to a joint-record league defeat.
Skipper James Bailey told the club website: "We know we let ourselves and the fans down.
"As a group, we want to apologise and give fans their money back."
Boss Darren Way added: "Saturday was never going to be easy but the manner of the defeat was totally unacceptable and I apologise to the supporters and take full responsibility for that.
"Paying supporters their money back is a collective decision - we're not happy with just apologising, but at the same time know our best apology will come on the pitch in the coming weeks."
The League Two side will release details of how fans can claim their refund on Monday.
Yeovil's players are not the first to reimburse travelling fans after an away day nightmare.
Sunderland's players refunded the 2,500 Black Cats supporters who saw their side fall to a humiliating 8-0 defeat at Southampton in October 2015.
In January 2016 Charlton's players did the same for the 166 who made the trip to see their side go down 5-0 at Huddersfield, in a performance that club captain Johnnie Jackson called "disgraceful".
Earlier this year, Bristol City's players refunded the 312 fans who made the 386-mile round trip to Preston North End to see the Robins lose 5-0.
Yeovil Town's players and staff have agreed to refund the 258 fans who travelled to their 8-2 opening day defeat at Luton Town.