The company had said after the fire that it plans to permanently shut down the 150-year-old facility in South Philadelphia, and lay off more than 1,000 workers.
Philadelphia Energy Solutions also filed for Chapter 11 bankruptcy last year.
It filed again on Sunday.
The termination date for workers is set for August 25.
Five days after the June 21 fire, which remains under investigation, Philadelphia Energy Solutions sent a notice to state labor officials that it will shut the plant down.
The fire significantly damaged equipment and systems at a complex that was already struggling financially, the company said.
The 150-year-old complex processes 335,000 barrels of crude oil daily into gasoline, jet fuel, propane, home heating oil and other products, according to the company. It started as a bulk petroleum storage facility in 1866 and began refinery operations in 1870.
The fire erupted in a tank containing a mix of butane and propane, a fire official said.
Five workers were treated for minor injuries.