The Tipperary side dominated the first half and led 2-8 to 0-5 at the break with the help of goals from Gearoid Troy and Darren Flood.
The impressive Flood — still U14 — hit 1-9 in all, but Midleton battled back in the second period, mainly through the accuracy of Liam Gosnell and Liam O’Shea.
Extra time was required, and the Cork side took over, adding nine points to Thurles’ three.
Midleton manager Tim Collins said: “The second half was outstanding after a shaky first half. Today was the best performance yet from this team, the second half was a massive comeback.”
L Gosnell (0-10, 1 pen, 2 frees), L O’Shea (0-8, 3 frees), E Dorgan, A Nganou, K Oke, G Millerick, S O’Leary Hayes (0-1 each).
D Flood (1-9, 2 frees, 1 65), G Troy (1-1), J Fallon, C Bowe, M Nally (0-1 each).
C Healy; C Evans, AW Barry, D Hogan; E O’Sullivan, S O’Leary Hayes, C Newland; G Millerick, L Smith; P Leahy, E Dorgan, K Oke; L O Shea, A Nganou, L Gosnell.
J Stack for C Healy (ht)
C Carew; J Ryan, E O’Gorman, R Darmody; M Nally, D Quirke, B McGrath; J Taylor, B O’Mara; K Connolly, G Troy, C Bowe; J Fallon, D Flood, A Cooney
Z Johnson for J Taylor (40)
Cathal Egan (Glen Rovers)