The demonstrators urged the parliament on Tuesday to take action and cancel the deployment of NATO missiles and troops in Turkey.
Anti-Patriot protesters also gathered in front of the German Embassy in Ankara.
The protest comes a day after four batteries of Patriot missiles, two each from Germany and the Netherlands, reached Turkey.
"Germany, take your Patriots and get out of Turkey," the protesters chanted on Tuesday.
A similar anti-Patriot protest was held in front of the US Embassy on Monday, where angry protesters condemned what they called Ankara’s interventionist policies towards Syria.
Also on Monday, a group of Turkish protesters tried to get through the barricades at Incirlik Air Force Base in Adana in protest to the arrival of Patriot anti-missile batteries. About 25 protesters were arrested.
The United States, Germany and the Netherlands have agreed to deploy two batteries of Patriot missiles each, under the command of NATO, along the Turkish-Syria border after the military alliance approved a request by Turkey for the deployment of the surface-to-air missiles in the border region on December 4, 2012.
The three countries will also send nearly 350 troops each to Turkey. A number of American, German and Dutch soldiers are already stationed in the country.
Turkish people have held several protests against the military plan.
The Syrian government has also censured the plan, calling it another act of provocation by the government of Turkish Prime Minister Recep Tayyip Erdogan.