British Transport Police (BTP), paramedics and fire rescue crews were called to the scene at Janefield Avenue, Johnstone, shortly before 6:30am. The railway line is located at the end of the street.
The 6am Glasgow to Ayr ScotRail service struck the car which was on the railway line.
A BTP spokesperson said: “Officers were called to the line in Johnstone at 6.26am this morning (15/08) following reports that a car had collided with a train.
"Paramedics also attended and the driver has been taken to hospital, thankfully his injuries are not believed to be life threatening. The vehicle has now been recovered, and the incident is not being treated as suspicious.’
A tweet from the official Scottish Fire and Rescue Twitter page said: "We mobilised nine appliances to Janefield Avenue, Johnstone after reports at 6.26am of a collision between a car and train.
"Crews removed the driver from the car into the care of paramedics. No other casualties. Crews escorted 9 passengers from the train. We remain at the scene."
ScotRail services between Glasgow and Ayr, Largs and Ardrossan Harbour were affected by the incident.
Network Rail have since reopened the line between Kilwinning and Paisley Gilmour Street. Train services are returning to normal but some services may still be cancelled, delayed or revised.
A Network Rail spokesperson said: “Our engineers are on site supporting the emergency services.
“No train crew or rail passengers were injured in this incident.
”The police are working to establish why the vehicle was on the railway.”
A ScotRail spokesperson said: “We will work with all the relevant authorities to establish the cause of the incident.”