The contest will pit Hank Roberts, a determined campaigner for a single teaching union and Gerald Imison, ATL deputy general secretary, against Dr Mary Bousted, the leadership's preferred candidate.
Dr Bousted, head of Kingston University school of education, has no union experience, but was chosen by the ATL's executive to succeed Peter Smith who retired on health grounds last year.
Mr Imison was considered for the post of general secretary but rejected by a selection committee headed by ATL president Mike Moore, despite assuming Mr Smith's role after his retirement.
He has been deputy general secretary since 1995 and has specialised in pay and conditions, winning praise from other union leaders for his role in workload talks.
Mr Roberts is well known to the unions as he is a member of the national executive of both the ATL and National Union of Teachers, and a member of the National Association of Schoolmasters Union of Women Teachers.
If elected, he has promised to overturn the union's support for last month's workload agreement.
Both Mr Imison and Mr Roberts had to win the support of six branches by today to challenge the leadership's decision.
"I am delighted that ordinary members will have a vote for the important post of general secretary. I support democracy and democracy has won," said Mr Roberts.
Voting papers will be sent to the ATL's 160,000 members on March 17.
The winner is expected to be announced on April 7.