Krasniqi made his senior debut with Mladá Boleslav in 2011 before signing for Turkish club Ankaraspor two years later.

After a brief spell with Melaka United, he signed for defending Malaysia Super League champions Johor Darul Ta'zim in 2020.

[3] On 2 March 2011, Krasniqi signed a contract until the end of the season with the Czech First League club Mladá Boleslav.

[11] Fourteen days later, he made his debut against Petaling Jaya City after being named in the starting line-up and scored his side's first goal during a 2–1 home win.

[13] On 28 February 2020, he made his debut in a 1–0 home win against his former club Kedah after coming on as a substitute in the 89th minute in place of Leandro Velázquez.

[15] On 13 March 2021, he made his debut in a 2–1 away defeat against Sydney FC after coming on as a substitute in the 85th minute in place of Angus Thurgate.

[18][19] In August 2022, Krasniqi moved to Thai League 1 side Khon Kaen United on a year-long loan.