The crash happened at the intersection of M and 25th at about 4:30 pm.
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Merced police say the motorcycle was hit by a van.
The 59-year-old rider was taken to the hospital where he later died.
Authorities are still trying to determine what led up to the crash, but say traffic had just resumed after coming to a stop for a train in the area.
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Alcohol or drugs are not believed to be factors in the crash, and the rider has not been identified
Merced officers are asking drivers to keep an eye out for motorcyclists on the road, and to drive carefully around them.