Mr Allen, a finance and accounting lecturer, will take up office at the 62,000-strong union's national conference in Blackpool, in May. He automatically becomes president in 2004.
Currently chair of Natfhe's black members' group and a former chair of the equal opportunities committee, Mr Allen says one of his priorities will be equality.
He said: "Natfhe has come a long way and is a good example of an organisation where everybody can aspire to every office regardless of their race, gender or sexuality.
"I hope my victory will encourage others to aspire to the highest positions in any organisation in the country."
Mr Allen, who is the second black person to hold the vice-president post, has been a Natfhe member for 15 years and is chair of the East Midlands region.
He has sat on the national executive council for nine months.
He is a member of the Trades Union Congress's race relations committee and sits on the commission for black staff in FE.
He said: "It is a concern that, particularly in FE, the opportunities for role models for students from ethnic backgrounds are very small.
"For example, in London, where 40 per cent of students are from ethnic-minority backgrounds, teaching staff do not offer a full reflection of the population.
"It is the same in the boardroom. The number of black governors is very small indeed."
He said he will use his office to try to address the "concerns of our members".
He identified these as including differences in the levels of pay between colleges and schools, increasing workloads and a lack of opportunities and progression.
He said: "We particularly need to engage the employers on the issue of workloads and to gain greater government funding of both further and higher education.
"I also want to see opportunities improved for all potential students and I am concerned that increases in student fees will damage efforts to widen access."
Mr Allen takes over the vice-presidency from Maureen O'Mara, a Grantham College lecturer, who becomes Natfhe's new president, succeeding Gerard Kelly.