The 26-year-old Spanish centre-back has been outstanding at the heart of the Rangers defence since signing from Osasuna last summer.
His club boss Walter Smith was also honoured, receiving Manager of the Year honours at the awards ceremony held at Glasgow's Kelvingrove Art Gallery.
Cuellar's honour came as no surprise, and he could follow it up by landing the PFA Scotland award on Sunday, and the Scottish Football Writers' Association prize next month.
Smith, 60, has revived Rangers' fortunes since returning for a second spell in charge of Rangers in January 2007.
His team are on course to end Celtic's reign as Scottish champions after two league titles in succession for Gordon Strachan's side.
MAIN AWARD WINNERS
Player of the Season - Carlos Cuellar (Rangers)
Manager of the Season - Walter Smith (Rangers)
Young Player of the Season - Aiden McGeady (Celtic)
Goal of the Season - Willo Flood, for Dundee United v St Mirren on December 15.
Under-19 League Player of the Season - Scott Anson (Kilmarnock)