The accident happened at the crossing on Palm near Dakota. Traffic was also tied up where the tracks cross Shields.
Fresno Police officers say they found a bicycle at the crash site that appeared to belong to the victim.
The train's conductor told investigators it may have been a suicide because the man appeared out of nowhere and was not on the bicycle at the time of the accident.
All the safety devices at the intersection appeared to be working. The victim's name will not be released until his family is notified.