Ford GoBike, which recently pulled its popular electric pedal-assist bicycles from its Bay Area short-term bike rental system, will bring them back in June.

The company suddenly removed the bikes from service in April, citing complaints about their brakes. Some riders complained that the brakes grabbed too aggressively, sending them over the handlebars or causing them to fall and injure themselves.

In all, GoBike pulled 1,000 e-bikes in the Bay Area, most of them in San Francisco, along with 2,000 more in New York and Washington, D.C. A report Monday said that e-bikes won’t return to New York streets until September.

But Julie Wood, a spokeswoman for Lyft — which has owned GoBike since last year — said San Francisco will see e-bikes back in its bike stations sooner.

“We expect e-bikes will return to the GoBike system in June,” she said in an e-mail. “We’re confident that putting rider safety first is always the right decision, and we’re working hard to design a world-class pedal-assist bike that we know our riders will love.”

The e-bikes that return will be a new design, she said, but she declined to provide details. The older e-bikes were designed by Motivate, an on-demand short-term bike rental business, which sold its nationwide bike-share operation to Lyft last July.

The return of the e-bikes is good news to commuters as well as to Lyft. The black e-bikes quickly caught on, especially with riders facing hillier routes around San Francisco. With the e-bikes out of commission, GoBike struggled to keep up with demand, leaving many bike stations empty.

GoBike tried to cope with the loss of e-bikes by repairing and recommissioning some damaged models of its blue, solely human-powered bicycles, which it refers to as its “classic model,” and by trying to shuffle the bikes around the city to stock heavily used stations.

Wood said San Francisco will get an entirely new fleet of e-bikes, and added that Lyft officials are still determining what to do with the original pedal-assist models.

Details on the return of the e-bikes, including dates and numbers of bikes, along with a list of their new features, will be forthcoming, Wood said.

Uber, Lyft’s main rival in the mobile-app ride-hailing business, acquired e-bike-rental company Jump Bikes last year. Uber has also invested in Lime, a short-term bike and scooter rental company.

Michael Cabanatuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com Twitter: @ctuan