Roy has been an integral part of both white-ball sides since England overhauled their approach to limited-overs cricket in 2015 but runs and fluency have been in short supply this year and the 32-year-old has paid with his place.
Having struggled with England throughout the summer Roy endured a miserable time in The Hundred, averaging 8.5 over six innings for Oval Invincibles and making three ducks.
Managing director of men's cricket Rob Key led the selection process, with head coach Matthew Mott and performance director Mo Bobat also included on the panel.
Lancashire's Phil Salt and Yorkshire's Harry Brook take their places in a 15-strong squad for the tournament in Australia, which takes place in October, but Dawid Malan could be promoted to open the batting to accommodate Ben Stokes' return in the middle order.
Fast bowlers Mark Wood and Chris Woakes have been included despite last featuring during the Test tour of the West Indies in March, with both men having completed long recovery programmes over recent months.
The duo's presence edges out Richard Gleeson, who is one of three travelling standbys alongside left-armer Tymal Mills and spinner Richard Dawson. All-rounder Sam Curran makes the cut in the main group.
England will take 19 players to Pakistan later this month for a seven-match T20 series - their first tour of the country since 2005 - with five uncapped players bolstering the travelling squad.
Will Jacks, a rising star with Surrey and Oval Invincibles, where he has thoroughly outshone Roy, is a notable name and he joins Jordan Cox, Tom Helm, Luke Wood and Olly Stone.
Chris Jordan (finger) and Liam Livingston (ankle) will both skip the Pakistan leg to work on their fitness for the World Cup, while Jonny Bairstow has been excused following a packed summer as an all-format regular.
Captain Jos Buttler will lead the trip but has already indicated that his calf injury will rule him out of the early stages of the series. Moeen Ali, who has Pakistani heritage, will take over as skipper for those games.
England's T20 World Cup squad: J Buttler (c), M Ali, J Bairstow, H Brook, S Curran, C Jordan, L Livingstone, D Malan, A Rashid, P Salt, B Stokes, R Topley, D Willey, C Woakes, M Wood.
Reserves: L Dawson, R Gleeson, T Mills.
England's T20 squad to tour Pakistan: J Buttler (c), M Ali, H Brook, J Cox, S Curran, B Duckett, L Dawson, R Gleeson, T Helm, W Jacks, D Malan, A Rashid, P Salt, O Stone, R Topley, D Willey, C Woakes, L Wood, M Wood.