He was born to Pyotr Georgievich Shchedrovitsky, a prominent Russian engineer, and Kapitolina Nikolayevna Bayukova, a physician and micro-biologist. His father was the Director of Orgaviaprom, the Research Institute for the Organisation of the Aviation Industry. Thus Georgy grew up interacting with members of the nomenklatura. In 1946, he started studying theoretical physics at the Physics Department of Moscow State University, where he developed an interest in the structure of scientific theories which in 1949 led to a transfer to the Philosophy Department where he soon focused on logic and methodology of science.
From the 1950s Shchedrovitsky developed a series of seminars which attracted mathematicians, psychologists, historians, architects, sociologists and physicians who focused their discussions of logical and epistemological issues. He became involved in the Moscow Methodological Circle set up by Alexander Zinoviev. In 1954, Shchedrovitsky took over leadership of the circle and played a prominent role in developing activity theory. Here the world was not seen as composed of human subjects and objects as in naturalistic theory. Rather objects are secondary constructs whose nature depends on the activity applied to them. Shchedrovitsky argued that activity was not so much an attribute of any individual but rather a system within which an individual is "captured" and which determines how they behave. Further he reflected on the task of the scientist, bearing in mind that a particular complex "object" might be viewed from a number of different scientific perspectives: thus the work of the scientist involves not just examining the object within a specific scientific framework, but must also involve the choice of methodology by which the subject is marked as a distinct subject of scientific enquiry.
In 1962 he joined Vadim Sadovsky and Erik Yudin, in creating the Interdisciplinary Seminar on Structural and Systemic Methods of Analysis in Science and Technology at the Commission on Cybernetics of the Academy of Sciences of the USSR which was headed by Aksel Berg. Shchedrovitsky headed the Seminar until 1976.
Shchedrovitsky presented an application of Vygotsky's activity theory with his development of organizational-activity games. These games were based on an application of Vygotsky's content-genetic logic to develop method of collective problem solving.