The tiny crustaceans are a naturally-occurring parasite that can cause disease and are responsible for many losses to wild and farmed fish stocks.
With resistance to chemical treatments rising, the Glasgow team has been looking at breeding resistance.
It has now come up with a new protocol to breed resistant fish and developed a mathematical model to predict outcomes.
Sea lice can cause skin lesions and increased susceptibility to infections by suppressing the host's immune system.
The parasite is estimated to cost the worldwide fish farming industry hundreds of millions of pounds a year.
Professor Michael Stear said: "Sea lice infection is a major threat to the health of farmed salmon and to the fish-farming economy.
"Our research has produced a practical tool for quantifying resistance to sea lice and shown that selection could substantially reduce the need for drug treatments.
"Selective breeding for sea lice resistance should reduce the impact of sea lice on fish health and thus greatly improve the sustainability of Atlantic salmon production."
The study outlining the Glasgow University model is published in the Royal Society journal Interface.
WWF Scotland director Lang Banks said: "There is no doubt that sea lice are a major problem for Scotland's salmon farming industry and that large amounts of chemicals are currently used to combat the problem.
"If we are to protect the wider environment, then finding ways to reduce the industry's reliance on chemicals is to be welcomed.
"However, as chemical use is only one of a number of environmental impacts from salmon farming, we need to see more farms sign up to the Aquaculture Stewardship Council's "responsible farming" labelling scheme, and pledge to operate more sustainably in all aspects of their operations."
Researchers at Glasgow University have developed a new way to protect farmed salmon from sea lice.