Most recently, a power failure and fire at the substation on Thursday stranded thousands of commuters during the evening rush.
SEPTA officials say the complete renovation of the substation will cost about $25 million and take three years.
SEPTA assistant general manager Jeffrey Knueppel said that the federal grant announced Tuesday would allow SEPTA to design and bid the Wayne Junction project, and that the transit agency would continue to seek more funding while it proceeded.
He praised the congressional delegation and Mayor Nutter for championing the project with transportation officials in Washington.
"This will improve service and reliability for millions of riders annually," SEPTA general manager Joseph Casey said.
The grant was from a pool of $500 million in TIGER (Transportation Investment Generating Economic Recovery) grants approved by Congress for fiscal 2012 and sought by local transportation agencies in applications to the Department of Transportation.
The Wayne Junction substation work is separate from a $30 million, three-year project to rebuild the nearby Wayne Junction passenger station, with elevators, new high-level platforms, restored passenger tunnels, and stairways, new lighting and signs, and a new heating and cooling system.
Contact Paul Nussbaum at 215-854-4587 or pnussbaum@phillynews.com.