The new Institute of Healthcare Management will bring together both the old Institute of Health Services Management and the Association of Managers in General Practice.
AMGP members voted overwhelmingly to back the move, with more than 70 votes in favour and one abstention. Members of the financially troubled IHSM had already voted in favour at an extraordinary meeting earlier in the week.
The organisations, which signed a partnership agreement last year, are now set to launch a new, combined, body - the Institute of Healthcare Management.
AMGP chief executive Rosey Foster said it was 'the right time for a new organisation' to 'unite primary care and NHS management'.
She added: 'Primary care must be part of the whole of NHS management because it is central to the functioning of primary care groups.' The IHM would 'start from scratch' with a new constitution.
IHSM director Karen Caines was equally positive, describing the move as 'a boost for health management as a whole' and a 'natural union' between organisations with 'common values and aims'.
Delegates admitted privately that the merger was effectively 'digging the IHSM out of a hole', given a recent history of static membership and difficult finances.
But in public they were positive. AMGP members believe they will benefit from the merger, despite the IHSM's troubles.
Luton practice manager Mary Sugars said: 'I think that the amalgamation is inevitable because the AMGP would struggle to survive by keeping its membership sufficiently high.
'The AMGP is an excellent organisation but we know that it has struggled to maintain its momentum.'
Leicester practice manager Bob Shearer warned of 'a danger that the AMGP will be overwhelmed'. With fewer than 2,000 members, the AMGP is a quarter of the size of the IHSM.