Dr Baker will take up the role of chair elect following the next council meeting in June, and will be formally appointed to succeed current chair Professor Clare Gerada in November.
In the election, Dr Baker received 37 votes and Dr Steve Mowle received 21 votes, out of a possible 67 votes.
Dr Baker said: 'I am delighted and honoured to be elected to such an important role at the RCGP. Later this year the NHS will celebrate its 65th anniversary in a landscape of financial austerity and an environment more complex and challenging than at any time in its history.
'This very week, news of the serious problems facing A&E units only serves to underline the desperate need for adequately resourced and properly integrated GP services.'
She added: 'I am more convinced than ever that GPs, and their professional body, have a crucial role to play in helping the NHS tackle the challenges of the years ahead. I look forward to playing my part in meeting these challenges.'
Dr Baker has been a GP since 1985 and practises in Lincolnshire. She served as RCGP honorary secretary from 1999-2009, and is currently a member of the RCGP Trustee Board, a nationally elected member of college council, and RCGP lead for emergency planning and preparedness.
She is also clinical director for patient safety at the Health and Social Care Information Centre.
In 2004, Dr Baker received a CBE for services to medicine and the RCGP Foundation Council Award for meritorious services to general practice in 2009.