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."

29 June 2015 Last updated at 11:41 BST
Mr Richards, 19, from Wednesbury, was among 38 killed when a Tunisian student linked to Islamic State extremists opened fire on a beach in Sousse on Friday.
He was a Walsall FC fan, football referee and student at the University of Worcester.
Chief executive of the Birmingham County Football Association, Chad Ehlertsen, said "it just makes you smile every time you think about Joel."
"He was just a leader of young people; a good organiser, a good communicator and an extremely talented young referee," Mr Ehlertsen said.

The private Caixin/Markit manufacturing purchasing managers' index (PMI) dropped to 47.8 in July from 49.4 in the previous month.
It is worse than a preliminary reading of 48.2 and is the fifth consecutive month of contraction in the sector.
A figure below 50 shows contraction in the sector and one above means growth.
The reading was the lowest since July 2013, when it fell to 47.7.
The disappointing results, which focus on small to mid-sized companies, come after the official survey over the weekend also showed signs of a slowing Chinese economy.
The official PMI, which focuses on larger companies, fell to 50 in July from 50.2 in June as growth stalled unexpectedly.
Bernard Aw, market strategist at trading firm IG said the data was not surprising and reinforced the view that there will be further weakness in the economy.
"I feel that the macro outlook of China - which is probably slowing further - has already been considered by the market," he said in a note on Monday.
The deterioration in China's vast manufacturing industry comes despite the government recently intervening heavily to boost the economy and stock market.
The central bank has already cut interest rates four times since November. It has also continuously eased lending rules for banks in aggressive measures to spur spending.
But manufacturers continued to cut production levels, with July seeing the fastest rate of contraction since November 2011.
Factory production - which contributes to the overall manufacturing activity reading- was at 47.1 in July, shrinking for the third month in a row.
Researchers at Glasgow University have developed a new way to protect farmed salmon from sea lice.
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One of the victims of the Tunisia beach attacks, Joel Richards, has been described as a leader of young people.
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Factory activity in the world's second largest economy, China, shrank the most in two years in July as new orders fell more than expected.