The decision handed the administration a courtroom win and dealt a setback to major business and university groups.
In a decision issued on Tuesday, US District Judge Beryl A. Howell said the case turned on constitutional and statutory authority rather than the economic impact raised by challengers.
She concluded that Congress had granted the president wide discretion, which he used to issue a proclamation framing the measure as tied to economic and national security concerns.
Trump signed the proclamation on September 19, requiring employers to make the US$100,000 payment before petitions for new H-1B visas would be processed, a move that drew sharp criticism from companies that rely on overseas hires for specialised roles.
The US Chamber of Commerce and the Association of American Universities, which represents dozens of US research universities, brought the lawsuit to block the policy.
The ruling is one of several legal tests facing the fee, including a separate, more recent challenge led by California and Massachusetts.
Employers typically pay several thousand dollars in fees for H-1B applications, meaning the new requirement would significantly raise the cost of recruiting foreign professionals.
Xinhua