Shell spokesman Thijs van Velzen says the fire started late Saturday and was extinguished by Sunday morning. Nobody was injured.
The Pernis refinery in Rotterdam's sprawling port is Europe's largest. It has the capacity to refine just over 400,000 barrels of crude oil per day.
The shutdown led to Shell burning off excess gases at the plant, a process known as flaring. The move sent large flames into the sky on Sunday.
Van Velzen says the cause of the fire is under investigation. He declined comment on the financial implications of the shutdown.