The Long Island Rail Road said it expected to resume normal service in time for Thursday morning's commute after clearing a derailed freight train near Hicksville that caused two days of cancellations and delays.

The derailment -- the third incident in just two weeks to cause major service disruptions on the LIRR -- impacted some 35,000 riders, more than a third of the railroad's 98,000 daily customers.

But the railroad said in a 10:25 p.m. statement Wednesday night that it expected to operate a "regular AM rush hour schedule of trains" Thursday morning after working through the night to complete repairs on one of two tracks shared by trains on the Ronkonkoma and Port Jefferson branches.

"LIRR work crews unloaded tons of construction debris from the freight car that had toppled on to its side and removed both the car and its wheel assemblies from the track area. The track -- including the electrified third rail -- was then rebuilt," the LIRR said referring to work done early Wednesday morning.

Wednesday night, after re-railing the second downed freight car, workers were removing it from the site, and rebuilding the damaged track and third rail, the railroad said.

The derailment came less than two weeks after a signal problem caused a morning rush-hour suspension of trains into and out of Penn Station, and less than a week after a crossing accident shut down service on part of the Ronkonkoma line.

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"You never like to have any events, but when you have multiple events, there is understandably a high level of frustration among our passengers," LIRR President Patrick Nowakowski said.

The derailment was one of numerous safety-related incidents involving New York & Atlantic Railway, the Glendale-based freight operator under contract with the LIRR. The Federal Railroad Administration in July announced it was conducting a safety review of the company after a collision between a freight train and a tractor trailer in Queens.

NY&A trains also derailed on the LIRR's tracks in April of this year and in May 2014.

Railway President Paul Victor said he didn't believe the train's crew wa "culpable" in Tuesday's derailment. "Although you may do everything in a safe manner, it doesn't mean that sometimes things don't go left when they should go right," he said.

With Ellen Yan