Stevenage will be on the road after the draw for the last 16 of the Papa John's Trophy.
Steve Evans' team were paired with League One Portsmouth after the regionalised draw conducted by Shaun Wright-Phillips and Kevin Nolan.
Boro fought past Peterborough United, Wycombe Wanderers and Tottenham Hotspur U21s in the group stage with three straight wins.
They then beat Arsenal U21s 3-2 on Tuesday night in the first of the knockout matches.
Pompey meanwhile had a win and two draws in their group alongside AFC Wimbledon, Crawley Town and Aston Villa U21.
They beat Ipswich Town 2-0 in the round of 32.
The tie at Fratton Park will be played in the week commencing December 12.
Papa John's Trophy round of 16
1.Salford City v Port Vale
2.Bolton Wanderers v Manchester United U21
3.Lincoln City v Everton U21 or Mansfield Town
4.Burton Albion v Accrington Stanley
5.Portsmouth v Stevenage
6.Cheltenham Town v Chelsea U21
7.Bristol Rovers v MK Dons
8.Plymouth Argyle v AFC Wimbledon
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