RailGo has pledged not to raise its fees to clients despite a cut in agent commission fees.
The online rail booking engine for business travel said the decision would affect its bottom line "quite considerably".
The decision to cut fees paid to agents was made by the Association of Train Operating Companies (ATOC).
From July 25, it reduced payments from 5% to 4% for bonded agents and to 3% for non-bonded agents.
The 4% will go down to 3% in March next year with ATOC aiming to cut it eventually to zero.
RailGo, which is owned by Flight Centre, also owners of FCm Travel, will continue to charge its corporate accountholders a "small card handling fee" plus £2 per transaction of the ticket is issued online or by post or £4.50 if they are collected at the station.
Nathan Cousins, RailGo's business development director, said: "ATOC's decision to cut commission rates and enforce us to take out a bond will affect our bottom line quite considerably.
"However we have resolved not to pass on any increase to our customers.
"By reviewing our own costs and negotiating various processing fees we have been able to hold our fees at the current rates for the rest of this year and throughout 2011."
Cousins added that it was important for RailGo, which launched last September, to "demonstrate to our clients that we are committed to keeping their costs as low as possible."
www.railgo.co.uk www.atoc.org