Boro's Under-23s were beaten by the odd goal in five at Blackburn in their second PL Cup group game on Friday.
Joe Gibson had fired Graeme Lee's young charges ahead inside the opening two minutes, but the home side hit back to turn the scoreline around before half-time.
Sam Burns quickly levelled matters and Jared Harlock scored with a near post finish four minutes before the break to give Blackburn the advantage.
Harlock had a hand in Blackburn's third when Harry Leonard scored on 73 minutes, but Boro rallied to pull one back late on courtesy of Isaac Fletcher.
Nottingham Forest are Boro's next opponents in the competition when they visit Bishop Auckland on Friday 12 November (7pm). Lee's side won their opening group game against QPR last month.