Scrapping practice boundaries represents the 'next stage of reform' said Mr Burnham, with patients encouraged to seek out the most convenient practices, allowing 'the extended hours journey to continue'.
He said that removing practice boundaries was intended not just to allow patients to visit a GP closer to work, but to drive patients to 'vote with their feet'.
Mr Burnham's comments came as the GPC revealed an alternative vision for making the boundary system more flexible.
The DoH also revealed this month that patients whose practices did not open extended hours would be offered evening and weekend appointments at neighbouring practices.
He said he had no plans to cap GP profits but warned the government would ratchet up pressure on GPs to invest more.
'Perhaps GPs have to think about investing, and services, in a different way.
'If they're not keeping up to date with services and facilities that people expect these days, they can expect to lose patients,' he said.
The BMA has said scrapping boundaries would be expensive and chaotic. But Mr Burnham told GP that location-based practice boundaries were 'not relevant any more'.
'The idea that "this is a closed parish" and "you can't go anywhere else" - we're not living in that world any more,' he said.
Scrapping boundaries would help continue the extended hours 'journey', allowing patients to choose the most convenient practices, or ones with a particular specialist, he said.
The health secretary also confirmed that Labour's policy on the private sector had not shifted, saying he would 'not flinch away' from alternative providers competing for new services.
In response, GPC chairman Dr Laurence Buckman reiterated his belief that the health secretary is intent on 'damaging' practices.
'(Scrapping boundaries) is not about patient choice, it's about damaging practices. He's quite keen to damage general practice. He wouldn't propose a system that hasn't been thought through or discussed if it didn't have some other intent.'
Dialogue between the GPC and the DoH appears to have broken down, despite Mr Burnham's claims that he works closely with the BMA.
'I thought we'd moved beyond threat and counter-threat, but obviously we haven't,' said Dr Buckman.
He called on Mr Burnham to open discussions with the BMA, rather than 'making threats'.
- Watch a video of the full interview with Mr Burnham online at healthcarerepublic.com/video