A little frustrated at the lack of first team opportunities available to him, Walsh moved to Middlesbrough (managed by his former teammate Bryan Robson) for £600,000 in August 1995, and played in 32 out of 38 Premier League games that season for a newly promoted side which went fourth in October but in the end could only manage a 12th-place finish due to a terrible run of form during the winter. The following season, however, he managed just 12 league appearances due to the emergence of Ben Roberts and the arrival of Mark Schwarzer. Middlesbrough also managed to reach both domestic cup finals that season. In the League Cup campaign, Walsh played in the quarter final victory over Liverpool, but was not selected in the final squad against Leicester City, who beat Middlesbrough in a replay. In the FA Cup run he played in the opening game of the campaign against Chester City, but would not feature in the tournament again as his teammates went on to lose the final 2–0 to Chelsea. Walsh never played first team football for the Riverside club again.