Judge Duncan Ouseley said on Wednesday that the Islamic Human Rights Commission (IHRC) had failed "by a very long way" to establish its case.
The commission had sought an injunction against the government, claiming Britain had aided "acts of terrorism" by Israel in its campaign against Hezbollah in southern Lebanon.
Last month, a stopover at Prestwick airport near Glasgow of US flights carrying missiles to Israel sparked intense criticism and vocal protests in Britain.
Several cargo flights bound for Israel subsequently landed for refuelling at RAF Mildenhall, a US-operated base in eastern England, rather than at the civilian Prestwick airport.
The commission, a London-based lobby group, had sought permission to sue the Civil Aviation Authority, the Foreign Office and Des Brown, the defence secretary.
Its lawyer, Peter Carter, said Britain had assisted in "disproportionate military attacks" by Israel, which killed and caused terror to people not directly involved in the conflict.
On Tuesday, Massoud Shadjareh, chairperson of the IHRC, described the organisation's action as "an attempt to force the relevant public authorities to respect the law ... but which our government refuses to abide by".