The move is aimed at encouraging the growth of the network and cutting off business for high-charging payday loan companies.
City Treasurer Paul Rooney will announce the rent cut at a meeting of the Association of British Credit Unions, which is holding its annual conference in the city.
In 2001, only 3% of people in the city were members of a credit union.
Today one in four Glaswegians is a credit union member, meaning 150,000 people are taking advantage of the services they offer.
Mr Rooney said: "That means 16% of all credit union accounts in Britain are held here in Glasgow.
"That has not happened by accident. Our credit unions have shown huge determination to grow, to professionalise their products and services."
The conference will be told the city council has gone out of its way to support and encourage the movement.
Mr Rooney said: "We have invested more than £8 million in the sector.
"We have also provided direct financial support for credit unions to move into high street premises and to meet staff and running costs."
As well as cutting rents by 50%, credit unions in the city already get 100% relief on non-domestic rates.
Mr Rooney added: "Glasgow is the credit union capital of the UK and we are very proud of how the sector has grown and flourished over the last decade.
"Our credit unions combat financial exclusion in our communities and can also play a key role in tackling the harm caused by the use of predatory, high cost payday lenders.
"By offering a real discount, we can help put credit unions at the heart of their communities where they will be more accessible to members old and new."
Recently, the city council decided to ban access to payday lender sites from all local authority computers.
The move affects the council's 20,000 staff and the thousands of people using computers in city libraries.
Around 100 sites offering high-cost, short-term loans have been added to an automatic blacklist, more often used to prevent inappropriate material such as pornography.
Council IT staff are also monitoring the internet and will bar access to new firms which come on the market.