Al Gore's film was sent to schools in England, Wales and Scotland
An Inconvenient Truth promotes "partisan political views" but it is not unlawful to show to students, Mr Justice Burton said.
He made the comments after a hearing in which Kent parent Stewart Dimmock asked for the film to be banned.
The judge said teachers must follow updated guidance when showing the film.
The guidance, updated this week by the government at the urging of Mr Justice Burton, is designed to prevent the film being wrongly "promoted" to children.
Mr Dimmock, from Dover, argued the film was unfit for schools because it was politically partisan and contains serious scientific inaccuracies, as well as "sentimental mush".
Although the judge is to give his judgement next week after a four-day case, he indicated what his ruling would be for the benefit of schools.
Children's Minister Kevin Brennan said: "The judge's decision is clear that schools can continue to use An Inconvenient Truth as part of their teaching on climate change in accordance with the amended guidance which will be available online tomorrow [3 October].
"Climate change is the greatest environmental challenge facing the world today. Schools have a special role to play in helping pupils understand its causes and in exploring if and how we should respond."
He said the updated guidance made "it clearer for teachers as to the stated IPCC [Intergovernmental Panel on Climate Change] position on a number of scientific points raised in the film".
He added that the key arguments in the documentary - "that climate change is mainly caused by man-made emissions of greenhouse gases and will have serious adverse consequences" - are supported by scientific opinion.