Two excavators were deployed at the Baiyunlu campus of Beijing No. 2 Experimental School in Xicheng District to remove the race-track.
The removal process will be completed in two days, state- run Xinhua news agency reported.
Students had a day off today, and will be back next Monday, it said.
Last month, many students at the school suffered from nosebleeds, dizzy spells and coughs after running on the track.
Tests on the track this week, nine months after it was put into use, showed excessive amounts of benzene substances and formaldehyde. Investigators also admitted to the existence of pungent smell in the track.