Florida Department of Transportation officials said a CXS train jumped the rails near State Road 46, south of a rail yard in Sanford around 1:30 a.m.
The train was traveling from Jacksonville to Orlando, said Kristin Seay, a spokeswoman for CSX.
"The train had three locomotives and 63 rail cars carrying mixed freight," Seay said. "Two locomotives and one car derailed. Crews are on site clearing the area now."
She said the derailment's cause is under investigation.
Southbound SunRail passenger trains were running on about a 15-minute delay Thursday morning as southbound trains had to share the northbound track between DeBary and Lake Mary, said SunRail spokesman Steve Olson.
"We can't switch tracks until we get past Sanford," Olsen said.
SunRail apologized for the delay on its Twitter account.
ATT. RIDERS: All #SunRail trains are receiving a 15 minute delay at this time due to traffic disruption. we apoplogize for the inconvenience— SunRail (@RideSunRail) September 4, 2014