The companies expect to begin production of the system in 2020 at a GM battery-pack facility outside Detroit, creating about 100 new jobs.
Honda and GM will invest a total of $85 million in the venture.
Honda and GM have collaborated on fuel cells and hydrogen storage since 2013. Dan Nicholson, GM's vice president of global propulsion, says costs have come down dramatically since then and the new fuel cell system has become smaller, lighter, less complex and more durable.
The companies also pledged to work with the government to increase the number of hydrogen refueling stations.