The programme sees the Men's Health Forum working with the Department of Health, NHS England and Public Health England to improve men's health.
The scheme also provides a way for the Forum to work a network of local voluntary and community sector organisations to help tackle men's health problems in their areas.
The Forum earned its place on the programme following an assessment process which saw fewer than one third of the 66 organisations and coalitions who applied being recruited for 2013-14.
Men's Health Forum CEO Martin Tod said 'This important partnership and the funding that comes with it will help us tackle the high rates of premature death in men and it will provide us with more opportunities to remind the public sector that they have a legal duty to tackle men's health.'
The Forum has worked with the Department of Health and other charities in the past but this new programme includes the new bodies NHS England and Public Health England and a new mix of organisations and coalitions.
Norman Lamb, the Care and Support Minister, said 'I am delighted that these 21 organisations will share £3.5m to help them work in partnership with the Department, NHS England and Public Health England as part of a new system-wide Health and Care Voluntary Sector Strategic Partner Programme for 2013/14.
The voluntary sector has a valuable role to play in improving health and wellbeing and this new programme will help develop and build strong and productive partnerships with the sector and support organisations to build capability more widely.'
The Men's Health Forum is now working with others on the programme on a co-ordinated plan of work for 2014/15.