The Bexley, south-east London GP takes up the role on a permanent basis after a 12-month stint as acting medical director for primary care.
Dr Kanani, who continues to work in frontline general practice, will now lead a national review of GP access promised earlier this year, with initial findings due in October.
Boris Johnson promised to 'drastically reduce' GP waiting times in his first speech as prime minister earlier this summer. Dr Kanani's appointment comes as the RCGP called for a sharp rise in GP training posts in England from the current 3,500 posts to 5,000 a year.
The review led by Dr Kanani will aim to improve 'patient access to general practice both in core hours and at evenings and weekends, and to reduce unwarranted variation in experience'. It will draw up proposals for a 'coherent access offer that practices and primary care networks (PCNs) will make both during the day and out-of-hours, for both physical and digital services'.
Dr Kanani has spoken out strongly in favour of the five-year GP contract and increased NHS funding through the NHS long-term plan - calling the promised £4.5bn rise in primary and community care funding by 2023/24 an 'unprecedented opportunity' for general practice.
The south-east London GP was appointed last year after former medical director Dr Arvind Madan was forced to resign, following his admission that he had posted provocative comments online about general practice under a pseudonym.
Dr Kanani said: 'I am delighted to have been appointed as medical director for primary care at NHS England and NHS Improvement. This is one of the most central roles in the NHS for delivering even better treatment and services for our patients and I would like to thank friends and colleagues across the NHS who have been so supportive over the past year since I took on the role in an interim capacity.
'It has certainly been a sharp learning curve, but over that year we have achieved so much - including publishing the NHS long-term plan with a core focus on primary care, agreeing an historic five-year GP contract, and building new relationships across the profession.'
On the access review, she added: 'Over the next year we will review how people access and navigate their care, begin to tackle the health inequalities that exist behind this and set out a credible path to building a diverse and inclusive workforce fit for the 21st century. Primary care is leading a culture change in the NHS, and I am so pleased to be a part of it.'
NHS chief executive Simon Stevens: 'GPs and primary care are vital to the success of the NHS and Nikki will provide great leadership as we work with GPs to tackle workforce pressures and expand access to services.'
Dr Kanani said earlier this year that sexism and sexual harassment have 'no place in our profession' after GPonline reported on senior female GPs' experiences within the BMA.