Monday's announcement by Progressive Conservative MP Greg Kerr follows the transfer of the ferry terminal property to the town.
The move comes ahead of the expected May startup of a new international ferry service between Yarmouth and Maine.
The federal funding will go towards the repainting of lines in the marshalling yard and will complete the demolition of the existing interiors of the building to remove mould and debris.
Other work to be completed includes the installation of new roofs and doors and an upgrade to the building's electrical, communications and heating systems.
Yarmouth Mayor Pam Mood says the funding and facility work means the service is one step closer to welcoming its first guests in May.