Allen started his career with Oxford United, and made his debut under Brian Horton in the 1991–92 Second Division campaign; he played fourteen games, helping the "U's" to avoid relegation. He made 31 appearances in 1992–93, as Oxford finished mid-table in the newly re-branded First Division. New manager Denis Smith played Allen in 45 games in 1993–94, though neither player or manager could prevent Oxford suffering relegation into the third tier. He played 36 games in 1994–95, as United missed out on the play-offs by six points. He played 24 games in the club's promotion winning 1995–96 campaign. Allen scored a total of 17 goals in 181 appearances in all competitions. Whilst at Oxford, he was capped twice for England at under-21 level, with both appearances coming in the 1995 edition of the Toulon Tournament, in 2–0 defeats to eventual finalists Brazil and France.