The lawsuit filed yesterday alleges investment in those companies violates the university's duties as a public charity.
The complaint asks the court to compel the Harvard Corporation, the governing body, to stop investing any of its USD 36.4 billion endowment in gas, coal and oil companies.
Harvard students have pressed the university to divest from fossil fuels as a way to slow climate change.
Spokesman Jeff Neal said university leaders agree that climate change must be confronted but "differ on the means" to do that.
In a letter to the Harvard community in October 2013, Harvard President Drew Faust called climate change "one of the world's most consequential challenges" but said she and her colleagues on the Harvard Corporation do not believe that divestment from the fossil fuel industry is warranted.