The legislation, part of the transportation and housing appropriations bill, was approved 68-30. It would deny federal subsidies to Amtrak if it doesn't change its rules. The House version does not include the provision.
Domestic airlines allow licensed gun owners to transport their weapons in their checked-through baggage. One senator said the gun measure "is going to put a severe burden" on Amtrak, CNN reported.
But the measure's sponsor, Sen. Roger Wicker, R-Miss., noted other railroads in the country manage to shoulder that burden.
"Only the federally subsidized Amtrak prohibits law-abiding American citizens from exercising their Second Amendment rights in checked baggage," Wicker said.
Amtrak spokesman Steve Kulm said the railroad was mulling its response.