Director Geoff Mawdsley said: "It makes little sense for health to be devolved to Holyrood, but the GMS contract negotiated on a UK basis when health policy in the different parts of the UK is diverging.
"This doesn't mean that ultimately the deal agreed would be all that different and there would be nothing stopping those involved in the Scottish negotiations from simply mirroring the English deal. However, importantly the final agreement for Scottish GPs would be made in Scotland reflecting Scottish circumstances and policies.
"It's time Scotland negotiated its own GMS contract, negotiated with Scottish circumstances in mind and designed to meet the unique needs of Scottish patients. Patients must come first and this change will help that goal be achieved."
Reform Scotland's recommendation comes after the Scottish Government announced plans to take greater control of contract in December last year.
A Scottish Government spokesman said: "Whilst now is not the time for a full renegotiation of the GP contract. the time is right for greater focus on Scottish priorities. Development of a more Scottish focused GP contract is just one strand of our work to ensure that general practice can play its full part in meeting the needs of Scottish patients in the years to come."