The protesters linked to Fatah party also chanted slogans against Qatar's Emir Sheikh Hammad bin Khalifa Al Thani in the city of Tulkarem on Thursday.
The protest came as Qatar has been under criticism for meddling in internal affairs of regional countries such as Syria.
Damascus says the West and its regional allies including Qatar, Saudi Arabia, and Turkey are supporting the militants fighting the government forces in the country.
Both Fatah and Hamas groups slammed the burning of the effigy of Qatar's emir, saying it did not reflect the opinion of the Palestinian leadership or people.
Acting Palestinian Authority chief Mahmoud Abbas said in a statement that Palestinians "respect the leaders of Arab countries and do not (seek to) interfere in their internal affairs."