The young midfielder has added goals to his ever-improving repertoire this season and was there when it mattered to provide a cultured finish from Andros Townsend's cross 10 minutes from time.
That made it three goals in four games for Walkes in the Barclays Under-21 Premier League as we made it four wins in five at the expense of a Boro team that had lost only once this term.
Rain poured down from start to finish at Middlesbrough’s Rockliffe Park base but that did little to dampen the performance of the team, who recovered from going 1-0 down on 15 minutes to create the better chances and dominate possession.
Townsend was at the heart of it, continually looking to take on his man and make things happen and it was no surprise when the winger zipped past Haydon Coulson and delivered for Walkes to land the points.
The pair combined in the first minute when Walkes headed just wide and in a lively start, goalkeeper Harry Voss made a fine point-blank save to deny Bryn Morris a minute later.
Harrison Chapman was bright for Boro and, having dragged a shot wide, he set up the home side's goal with a run from deep on 15 minutes. He was stopped in the box but the ball ran to Joao Morelli, who drilled low past Voss from the right angle.
Shaq Coulthirst volleyed straight at Joe Fryer as we pressed on, Shayon Harrison curled over, Emmanuel Sonupe fired into the side-netting and Townsend's late piledriver was deflected into Fryer's hands. At the other end, Chapman looped a header just wide as Boro held onto their 1-0 lead at the interval.
We controlled the second half and the Townsend-Walkes combination was there again on 56 minutes, but this time Walkes didn't get enough power on his effort to trouble Fryers.
We levelled on 58 minutes thanks to a perfectly-weighted pass from Milos Veljkovic – back at the club he spent time on loan at last season – into the path of Coulthirst, who simply guided the ball past the advancing Fryers and home.
Voss was ready for what was his only save of note in the second half on the hour as the dangerous Chapman worked a yard in the box but the goalkeeper showed good reactions to touch over.
Townsend's influence on the game continued to grow as conditions got tougher. The ball began to stick as water settled on the playing surface but that wasn't stopping the England man, who broke away with Coulthirst to set up Filip Lesniak, whose goalbound effort was blocked. Townsend and Lesniak then opened it up for Walkes, who didn't connect properly this time and Townsend then dragged wide after cutting in from the left.
Neither he nor the team was going to be denied though and the winner arrived on 80 minutes. Townsend raced away from Coulson and charged towards the box before crossing from the byline for Walkes, who timed his run to perfection to cushion home a volley.
Middlesbrough had one final chance to level in injury time when Matthew Elsdon met Arnal Jakupovic's overhead kick but he couldn't find the power to trouble Voss.
Middlesbrough U21s: Fryer, Johnson, Fry, Elsdon, McGinley (Coulson 68), Tinkler (c), Chapman, Morris, Morelli (Jakupovic 72), Maloney (Wheatley 81), Mondal. Substitutes (not used): Coddington, Jowers.
Spurs U21s: Voss, Walker-Peters, Georgiou, Lesniak, Veljkovic (c), Amos, Townsend, Walkes, Coulthirst (Goddard 88), Harrison (J Pritchard 83), Sonupe (Miller 77). Substitute (not used): McDermott (GK).
NEXT MONDAY: Watch live coverage of our Under-21s' clash with Southampton at Stevenage, completely free on Spurs TV! On air from 6.30pm, we kick-off at 7pm.