Less than a week on from the historic referendum, which saw voters back quitting the EU by a slim majority, Dr Maureen Baker said the NHS funding claim may have had a 'significant impact' on the result.
She said patients who feared for the future of the NHS - with trusts in deficit, a growing workforce crisis and longer waits for appointments - may have been persuaded to vote leave to secure the £350m extra NHS funding.
Dr Baker said: 'The British public – our patients – voted last Thursday to leave the European Union.
'Many of those who did vote to leave will have been influenced by a campaign that played up the amount of money that the UK pays to be a member state of the EU, and suggested that this money could be spent on the NHS instead.
'With the NHS – and general practice at its heart - held in such high regard amongst the public, and at a time when patients are struggling to make a GP appointment due to soaring demand, insufficient resources and a stagnating GP workforce, it is possible that these messages could have had a significant impact on the result.'
Dr Baker called earlier this week for those who made the £350m claim to 'deliver or resign'. House of Commons health select committee chair Dr Sarah Wollaston, a former GP, has also said she will hold to account Brexit campaigners over NHS funding claims.
Speaking on the BBC's Andrew Marr show on Sunday, Brexit campaigner and senior Conservative Iain Duncan Smith said the government would decide whether funding clawed back from the EU would go to the NHS. He said 'a significant amount' of funding previously given to the EU could top up NHS funding, but admitted 'it was never the total' £350m that would go to the health service.
Dr Baker added: 'The priority for the college is to make sure that general practice, which makes 90% of all NHS patient contacts, receives its fair share of any new money made available for the health service.
'GPs and our teams make well in excess of 370m patient consultations a year – 60m more than five years ago – yet the number of family doctors has increased only slightly and over the last decade, investment in our service has significantly decreased.
'In England, the GP Forward View is a lifeline for our profession and the care we can deliver to patients. The College will be working to ensure that pledges to increase investment in our service and build our workforce are implemented as a matter of urgency, regardless of any implications that might arise following the decision to leave the EU.
'In Scotland, Wales and Northern Ireland the college will continue to pursue the goals of our Put patients first: Back general practice [campaign], calling for more investment in general practice, and for more GPs and practice staff, as a matter of urgency.
'Only with a strong general practice service will the NHS be able to deliver the care our patients need and deserve – regardless of whether the UK is a member of the EU, or not.'