The collision occurred on Monday evening near Shibin al-Qanatir, north of the capital, according to police officials.
Although it was not clear what caused the crash, security sources told Reuters news agency that the trains had been travelling in opposite directions on the same length of track and collided head-on, causing several carriages to derail.
Officials said many deaths were avoided because the passenger train's third-class section was largely empty.
The accident comes just two weeks after a passenger train rammed into the back of another train parked at a station in Qalyub, in the same province as Shibin al-Qanatir, killing 58 people.
The crashes have caused public anger in Egypt over the country's failing rail infrastructure.
Mohammed Mansour, the transportation minister, later acknowledged that the rail system was in need of a major overhaul and was severely underfunded.
The government has since approved an allocation of $860m to develop the rail infrastructure, plus another $600m in loans to the sector.
Egypt has poor safety records on its railways and there are several fatal accidents each year, usually blamed on badly maintained equipment.
The country's worst recent rail accident took place in February 2002, when a train heading to southern Egypt caught fire, killing 363 people.