The Manchester United striker failed to receive enough votes from members of FifPro, the worldwide players’ union, to be one of the 55 nominees.
Until now, Rooney had received a nomination every year since the award’s inception in 2005. He has been named in the final XI on one occasion in 2011.
Andrea Pirlo is the other former ever-present to miss out. Cristiano Ronaldo and Gianluigi Buffon are now the only two players to have been nominated by FifPro’s members every year.
Hector Bellerin, N’Golo Kante, Dimitri Payet and Jamie Vardy are all included after impressive displays during the 2015/16 Premier League season.
Riyad Mahrez, however, is not among the 55 players nominated, despite winning the PFA's Player of the Year prize and featuring in promotional material for the FifPro award.
Borussia Dortmund's Pierre-Emerick Aubameyang is another high-profile absentee, but Mesut Ozil returns to the list having been omitted in 2015.
The shortlist is compiled by votes from FifPro's 25,000-strong membership, who are asked to select one goalkeeper, four defenders, three midfielders and three forwards.
The 2016 Fifa FifPro World11 will be announced at the Ballon d’Or ceremony, now renamed ‘The Best Fifa Football Awards’, in Zurich on 9 January 2017.
2016 Fifa/FifPro World11 shortlist
Claudio Bravo (Chile/FC Barcelona/Manchester City), Gianluigi Buffon (Italy/Juventus), David de Gea (Spain/Manchester United), Keylor Navas (Costa Rica/Real Madrid), Manuel Neuer (Germany/FC Bayern Munich).
David Alaba (Austria/FC Bayern Munich), Jordi Alba (Spain/FC Barcelona), Serge Aurier (Côte d’Ivoire/Paris Saint-Germain), Hector Bellerìn (Spain/Arsenal), Jerome Boateng (Germany/FC Bayern Munich), Leonardo Bonucci (Italy/Juventus), Daniel Carvajal (Spain/Real Madrid), Giorgio Chiellini (Italy/Juventus), Dani Alves (Brazil/FC Barcelona/Juventus), David Luiz (Brazil/Paris Saint-Germain/Chelsea), Diego Godin (Uruguay/Atlético Madrid), Mats Hummels (Germany/Borussia Dortmund/FC Bayern Munich), Philipp Lahm (Germany/FC Bayern Munich), Marcelo (Brazil/Real Madrid), Javier Mascherano (Argentina/FC Barcelona), Pepe (Portugal/Real Madrid), Gerard Pique (Spain/FC Barcelona), Sergio Ramos (Spain/Real Madrid), Thiago Silva (Brazil/Paris Saint-Germain), Raphael Varane (France/Real Madrid).
Xabi Alonso (Spain/FC Bayern Munich), Sergio Busquets (Spain/FC Barcelona), Kevin De Bruyne (Belgium/Manchester City), Eden Hazard (Belgium/Chelsea), Andres Iniesta (Spain/FC Barcelona), N’Golo Kante (France/Leicester City/Chelsea), Toni Kroos (Germany/Real Madrid), Luka Modric (Croatia/Real Madrid), Mesut Ozil (Germany/Arsenal), Dimitri Payet (France/West Ham United), Paul Pogba (France/Juventus/Manchester United), Ivan Rakitic (Croatia/FC Barcelona), David Silva (Spain/Manchester City), Marco Verratti (Italy/Paris Saint-Germain), Arturo Vidal (Chile/FC Bayern Munich).
Sergio Aguero (Argentina/Manchester City), Gareth Bale (Wales/Real Madrid), Karim Benzema (France/Real Madrid), Cristiano Ronaldo (Portugal/Real Madrid), Paulo Dybala (Argentina/Juventus), Antoine Griezmann (France/Atlético Madrid), Gonzalo Higuain (Argentina/Napoli/Juventus), Zlatan Ibrahimovic (Sweden/Paris Saint-Germain/Manchester United), Robert Lewandowski (Poland/FC Bayern Munich), Lionel Messi (Argentina/FC Barcelona), Thomas Muller (Germany/FC Bayern Munich), Neymar (Brazil/FC Barcelona), Alexis Sanchez (Chile/Arsenal), Luis Suarez (Uruguay/FC Barcelona), Jamie Vardy (England/Leicester City).
Original source: Rooney left off World XI shortlist for first time