Burnley: Jakovlevs, Dummigan, Azam, Daly, Holt, Whitmore, Jackson (Crawford 86), Lowe, Massanka (Metz 76), Bianga (Wilson 83), Nuttall.
Winger Bradley Jackson put Burnley back ahead before Alex Whitmore tapped in the third in the 85th minute to celebrate his 18th birthday in style.
An inspired team talk from Terry Pashley seemed to have worked because the young Clarets played some great football in the second half.
Former Manchester United youngster Luke Daly opened the scoring for the Clarets six minutes before half time, before the Wrexham equalizer two minutes later.
After two successive draws, the youth team got back into winning ways with a 3-1 win at Wrexham.