The Argentinean has netted 29 times so far in all competitions for City which helped him become the fans' top choice for the gong.
The award, in association with the MCFC Supporters Club, was presented to striker at end of season award ceremony held at the Etihad Stadium.
Aguero also took home Goal of the Season for the first of his two away to Norwich.
Not to be outdone, Aguero's team-mate David Silva was recognised for a fine season under Roberto Mancini with the Players' Player of the Year award.
City are just two big wins away from finishing top of the league for the first time since 1968.
Mancini's men currently lead the Premier League on a healthy goal difference over champions Manchester United with only games at Newcastle on Sunday and relegation-threatened QPR the following week left to go.