The protest, against China's treatment of the minority, was outside the Turkish Olympics House.
Chinese authorities have been accused of facilitating forced labour by detaining around a million Uyghurs and other primarily Muslim minorities in camps since 2016.
China initially denied the camps existed, but has since said they are vocational centers and are designed to combat extremism. It denies all accusations of abuse.
Protester Abdurrahman Taymaz said China is "committing genocide" and that the word needs to "wake up".
About 50,000 Uyghurs - with whom Turks share ethnic, religious and linguistic connections - are believed to reside in Turkey, the largest Uyghur diaspora outside Central Asia.