It will be the first in the North West and just the third in the UK to be run by an independent firm under a new scheme accused of privatising the "frontline of the NHS" by the back door.
The revelation has angered doctors' group Keep Our NHS Public, which last night warned putting the focus on profit would turn patients into "commodities".
It comes after a practice in Barking and Dagenham became the first in the country to announce it will be taken over by a private firm last month.
Essex company Care UK was awarded a deal, believed to be worth £5m over five years, to provide primary care services free to 7,000 NHS patients there from July.
Then earlier this month, villagers lost a High Court battle to stop US private firm United Health Europe taking over a second local practice, in North Eastern Derbyshire.
The new contracts, called Alternative Provider Medical Services (APMS), are being piloted in six areas including a third in Merseyside.
Services will still be offered free to patients, and Primary Care Trust managers in South Sefton say it will boost efficiency and improve the scope for longer opening hours.
But campaigners say that it will drain resources from the NHS by attracting money, doctors and nurses into the private sector.
Alex Scott-Samuel, senior lecturer in public health at the University of Liverpool, is also on the committee of KONP's Merseyside branch.
"I'm deeply concerned about the damage this is doing to the NHS through introducing the private sector initially into hospital services and now into primary care.
"This is one more nail in the coffin of front line care," he said. "Firstly companies are doing this work primarily to make a profit, secondly they have no experience of primary care.
"Not only will it draw doctors and financial resources away from the NHS, it will inevitably be a poorer quality of care that is provided. It's also about changing the whole quality of the NHS from being part of the Welfare State providing services that we all feel part of, to reducing people and their health to commodities.
"It's the commercialisation of the welfare state and it's carrying on the damage that the Thatcher government started."
This week, Dr Hamish Meldrum, chairman of the British Medical Association GP committee, told its annual conference the pace of health reform should slow down.
And other doctors warned encouraging private firms into the GP market would lead to the "fragmentation of the NHS".
Care UK has already come in for some heavy criticism from KNOP chairman and lecturer at Edinburgh University, Allyson Pollock.
She accused the company of having "very little experience" of providing direct services for patients.
It is not known if Care UK or United Health Europe have tendered for the Sefton contract.
The names of all companies involved are being kept heavily under wraps, and it is possible a voluntary group or consortium of GPs could win the deal under the APMS terms.
Both the Department of Health and local Trust managers say East Sefton was chosen because it is traditionally difficult to attract GPs to work there, and several doctors are due to retire soon.
No specific site has been chosen yet.
It is understood all suggestions by companies wanting to run the clinic will be considered.
A spokeswoman for South Sefton primary care trust said: "The contract for this service was put out to tender late last year, inviting bids from a range of primary care providers including independent general practitioners and the wider independent sector and voluntary sector.
"This is an area where there is under-provision of primary care services, with difficulties in attracting GPs and other primary care clinicians to the area.
"It is anticipated that the difficulties will continue due to expected GP retirements. The purpose of the exercise is to improve the levels and quality of service provision.
"The process is on-going and we are therefore obliged to keep confidential the identity of those involved at this stage.
"Since the creation of the NHS, most GPs have been independent contractors. The Alternative Provider Medical Services (APMS) contract is simply another way to provide the same primary care services as those provided by traditional GPs.
"The involvement of the independent sector in health care provision is expected to improve standards and provide patients with services that are more convenient, with early-morning, late-evening and weekend surgeries."
Others though, are not so sure. KNOP's national spokesman, John Lister, referred to a deal for Canadian-owned Interhealth Care Services to operate a £146m orthopaedic ISTC (Independent Sector Treatment Centre, Merseyside and Cheshire's first) in Runcorn.
He said: "The private sector are coming in and they are picking and choosing what areas they want to go into.
"They don't want anything messy like emergency care, they want fast admissions, treatment and discharge like a factory production line.
"Initially, it appears it's a great way to increase capacity, but in the end all it is doing is taking capacity away from the NHS."
He added: "Gradually it means the private sector is going to have quite a large controlling stake in the NHS and you lose the focus on patient care being the driving force."