The milestone serves as yet another warning sign that hydrogen is failing to gain traction in the consumer automotive market.
Toyota's Mirai has finally surpassed 3,000 sales in California since arriving on the market in the second half of 2015.
"Toyota remains at the forefront of developing and deploying hydrogen fuel cell technology, and we believe strongly in its potential to help realize a more sustainable and zero-emissions society," Toyota Motor North America executive VP Bob Carter says.
The Mirai is said to dominate the niche segment, accounting for 80 percent of all hydrogen fuel cell vehicles in the US. If true, there may only be around 3,750 FCVs in the entire country.
To put the number into perspective against other low- or zero-emissions vehicles, Toyota's Prius counted more than 245,000 sales in the US in the two years ending December 2017. The Nissan Leaf, meanwhile, achieved more than 25,000 deliveries and Tesla is estimated to have sold more than 95,000 units in the US.
With just 31 hydrogen refueling stations across the entire state of California, Toyota appears to recognize the need for more infrastructure. The Japanese automaker has partnered with Shell and FirstElement Fuels to expand stations in California. A separate initiative aims to engage the East Coast with a dozen stations from Boston to New York City, though zero-emissions enthusiasts will still need a pure battery-powered EV to take a road trip from coast to coast.