His first team was Naftex Burgas. He was first loaned to CSKA Sofia during 2004, but bought in the summer of 2005. In 2007, for a period of six months, Stoyko was loaned out to Lokomotiv Plovdiv.
In August 2008, he went to play for Spartak Varna.
On 5 March 2011, Sakaliev scored a last-minute goal against Vidima Rakovski in an A PFG match. In the summer of 2011 Sakaliev signed contract with Eastern B group side Neftochimic 1962.
On 17 September 2011 he scored twice from penalties as Neftochimic finished 2:2 with Botev Plovdiv. Sakaliev has just signed a contract with Kercem Ajax, playing in the first division on the island of Gozo, Malta.
In late May 2013, Sakaliev announced his retirement from football.
In 2004 Stoyko Sakaliev played in four matches for Bulgaria national football team Sakaliev was formerly married to Julvena and they have a daughter, named Liubomira. He is known for his elaborate pranks on teammates and other public figures during his playing days.