The Seagulls have two evening matches at the Amex Stadium this week which are likely to be disrupted.
The club say up to 12,000 fans travel to and from games by train to Falmer Station and that ticket sales for matches have been “slow”.
Falmer Station will not be served in the evenings during the course of the strike by RMT union members.
Hundreds of Southern trains have been cancelled following a row over plans for drivers, not conductors, to operate carriage doors.
Brighton face Colchester in the EFL Cup on Tuesday before hosting Nottingham Forest in the Championship on Friday, with both matches due to kick off at 19:45 BST.
As part of Southern’s revised timetable during the strike, the last train to depart from Brighton for Falmer pre-match will leave at 18:15 BST, with the last return back to the city centre leaving at 18:45 BST – almost three hours before the games are scheduled to finish.
As well as lost revenue totalling £250,000, Brighton claim they will also have increased costs of £50,000 providing replacement buses, additional park-and-ride facilities and extra stewarding.
Brighton director Martin Perry has written to three local MPs describing the disruption as “totally unacceptable”.
“Our success relies totally on us having a reliable, efficient, good quality train and bus service,” he wrote in an open letter published on the club website.