Allen joined Millwall in March 1990 for £400,000, spending three years there before moving to Newcastle United for £300,000 in August 1993, in time for their first season in the FA Premier League following their promotion as Division One champions. He started off well on Tyneside, scoring seven goals in 12 games, before suffering a serious ankle injury. He made just one more appearance for the Magpies, and after a long struggle to regain full fitness, he retired from playing aged 28 in December 1995.