City initially took the lead thanks to Nabil Touaizi's goal in the 52nd minute, but the visitors responded quickly and equalised with a penalty kick just eight minutes later.
Middlesbrough took the lead in the 72nd minute, but City fought until the end when captain Eric Garcia tapped in the ball just three minutes before the whistle to make it 2-2.
Manchester City were unlucky not to score in the first half.
Middlesbrough ‘keeper, Zach Hemming, had a great game and worked tirelessly to prevent City from converting.
Hemming’s heart was sent racing just five minutes into the game when Tommy Doyle struck a long range effort towards the top right corner, but the midfielder’s effort soared just over the crossbar.
Ian Poveda went close to scoring multiple times, particularly after a long fleeting solo run – where he dipped, dodged and weaved his way through the ‘Boro defence, but he was unable to convert.
City’s goal finally came seven minutes into the second half when Nabil Touaizi converted Henri Ogunby’s perfectly timed cross to put City 1-0 up.
The visitors were soon back on level terms, though, after Doyle collided with Stephen Wearne in the box and a penalty awarded.
Stephen Walker scored from the spot on the hour.
The penalty gave the visitors a new found confidence and they eventually took the lead in the 72nd minute when ‘Boro substitute Gabby McGill's shot found the target.
City continued to fight right until the end, and it was skipper Garcia's shot that levelled the scoreline up in the closing moments of the game. After a number of players had attempted to score the second, the Spaniard was on hand to ensure the Blues took a point from the game.
How they lined up
Curtis Anderson took his place in goal, with a back four of Ryan Corrigan, Colin Rosler, skipper Eric Garcia and Jeremie Frimpong.
Iker Pozo, Felix Nmecha and Tommy Doyle made up the midfield, while Ian Poveda and Henri Ogunby flanked Nabil Touaizi up front.
What it means
The result means that City's point tally increases to 26 in the league table.
Next, Gareth Taylor’s side head to Blackburn Rovers on Saturday 3 February for another Under-18s Premier League clash.