SAN FRANCISCO—In the digital age, it's not enough to craft an airtight arbitration agreement. You have to place it where customers can actually find it.

That, in essence, was the ruling from federal judge in San Francisco on Monday who denied Uber's request to route a class action lawsuit into arbitration in a case brought by a customer challenging the way the ride-hailing company assesses certain cancellation fees.

U.S. District Judge Richard Seeborg of the Northern District of California held that Uber's terms of service included a valid agreement to hash out customer disputes in arbitration. But the judge concluded that a link to that agreement presented to customers signing up for the app was obstructed by a pop-up type-pad when customers entered their payment and account information. The judge wrote that the flow of the registration process was “of paramount importance” to determining whether a customer using the Android version of Uber app had assented to the user agreement.