Steve Sinnott, from the right of the union and a supporter of Doug McAvoy, beat Mary Hufford, the incumbent left-winger, by 25,763 votes to 16,512.
Marian Darke, who broke away from the Broad Left (the McAvoy faction) to stand for election on an equal opportunities ticket polled 9,033 votes.
Mr McAvoy, who narrowly beat off Mary Hufford's challenge for the leadership earlier this year, will be 60 when his five-year term ends. If he decides to stand down, Mr Sinnott will be in pole position to take over. However, rumours at Hamilton House say Mr McAvoy may try for another term.
"It is wonderful for the union to have a united team at the top, and Doug's strengths and my strengths will work together to further the union. The scale of my success means that I have a considerable mandate across the membership, " Mr Sinnott said.
He admitted the biggest challenge will be the boycott of national curriculum assessment and testing. The union is the only one to continue with the boycott and may not be able to count on parental support for the third year running.
The other unions believe the Government has made sufficient changes and reduced the workload. But Mr Sinnott said his union's recent survey of members' views of the tests showed massive opposition to them.
He said: "I look forward to meeting Gillian Shephard and putting to her the view of our members."
Mr Sinnott, 42, born in Liverpool, became president earlier this year, and was the first to have attended a comprehensive school. His first teaching post was at Shorefields school, Toxteth, Liverpool, where he taught humanities. He later moved to Broughton High School, Preston, and became head of economics and business studies.
With his sharp suits and shiny shoes, he has not always endeared himself to the radical elements of the union. And, following the election of Tony Blair as Labour leader, he looks like a man whose time has come. That said, the NUT, which shared a close relationship with Ann Taylor, the former Labour shadow education minister, has already taken exception to the support David Blunkett, her successor, has given exam league tables. "I'm sure we can have a good working relationship with David Blunkett; but if we don't agree with him we will say so," he said.
Mr Sinnott's successor as president will be decided by the union's national executive next month.