Henderson, who won his maiden senior international cap as Fabio Capello's side slumped to a 2-1 home defeat to France in November, has dropped back into the Under-21 squad for next Tuesday's friendly with Italy.
Stuart Pearce has also selected Middlesbrough full-back Joe Bennett, who is involved at Under-21 level for the first time, and Boro goalkeeper Jason Steele.
Henderson's demotion was widely expected, despite the Sunderland-born midfielder having made his senior bow less than three months ago.
Capello named an extremely youthful squad for the France friendly, but with next Wednesday's game in Copenhagen serving as a warm-up for March's European Championships qualifier in Wales, the England boss will select a greater proportion of more experienced players.
Henderson is one of the more notable absentees, and will instead drop back down to Pearce's squad for a friendly in Empoli.
The 20-year-old has still only won five Under-21 caps, and Capello is keen to see him gain more experience at that level before another elevation to the senior squad.
Henderson is the only Sunderland player to have played in every Premier League match this season, but has struggled to produce his best form in the last month or so.
Bennett's selection is something of a surprise, but merely underlines how much progress the Northallerton-based full-back has made this season.
Bennett, who was part of the Under-19s squad at the 2009 European Championships, was repeatedly overlooked by Gordon Strachan, but has started Boro's last 14 league games under Tony Mowbray and repeatedly caught the eye.
We're missing a number of players through injury, but it will give me a chance to look at a few new players, said Pearce. Jay Rodriguez has been playing well for Burnley and deserves an opportunity with the Under-21s, likewise Joe Bennett at Middlesbrough has previously played for the Under-19s and his performances for Tony Mowbray have been impressive.
Newton Aycliffe-born Steele will hope to win his second Under-21 cap as part of a squad that also includes Kieran Gibbs, Micah Richards and highly-rated Southampton youngster Alex Oxlade-Chamberlain.
The 17-year-old Oxlade- Chamberlain was reportedly a target for Manchester United and Arsenal during the transfer window.
Pearce said: I saw Southampton play Manchester United in The FA Cup on Saturday and Alex Chamberlain is showing a lot of promise so we thought we'd bring him into the squad.''
Squad: Fielding (Blackburn), Loach (Watford), Steele (Middlesbrough); Bennett (Middlesbrough), Gibbs (Arsenal), Kelly (Liverpool), Mee, Richards (both Manchester City), Smalling (Manchester United), Tomkins (West Ham), Walker (Tottenham); Albrighton (Aston Villa), Cork (Chelsea), Delph (Aston Villa), Oxlade-Chamberlain (Southampton), Henderson (Sunderland), Lansbury (Arsenal), Muamba (Bolton), Rodwell (Everton), Sinclair (Swansea); Delfouneso (Aston Villa), Rodriguez (Burnley), Sturridge (Chelsea).