Latics beat Lincoln 1-0 in second round at the weekend
Stevenage will travel to Wigan Athletic in the FA Youth Cup third round.
Wigan knocked out Lincoln City with a 1-0 victory on Saturday in the second round of the competition.
Boro booked their place in the third round following a 4-2 win on penalties against Cambridge United last Wednesday.
The third round matches are scheduled to be played by December 19.
Third round draw
Wigan Athletic v Stevenage; Coventry City or Crewe Alexandra v Stoke City; Manchester United v Queens Park Rangers; Blackburn Rovers v Newport County or Southend United; Swansea City v Sheffield Wednesday; Oldham Athletic or Morecambe v AFC Bournemouth; Charlton Athletic v Millwall; Notts County v Luton Town; Arsenal v West Bromwich Albion; Nottingham Forest v Brighton & Hove Albion; Derby County v West Ham United; Mansfield Town v Sunderland; Hull City v Norwich City; Exeter City v Bolton Wanderers; Ilkeston v Newcastle United; Tottenham Hotspur v Rotherham United; Wolverhampton Wanderers v MK Dons; Reading v Chesterfield or Sheffield United; Liverpool v Ipswich Town; Worthing v Middlesbrough; Southampton v Birmingham City; Portsmouth v Manchester City; Everton v Aston Villa; Carlisle United v Preston North End; Leicester City v Cheltenham Town; Burnley v Metropolitan Police; Chelsea v Huddersfield Town; Watford v AFC Wimbledon or Ebbsfleet United; Brentford v Leeds United; Bristol City v Cardiff City; Fulham v Bury; Accrington Stanley v Crystal Palace.
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