Scheele was born in Stralsund, in western Pomerania, which at the time was a Swedish Dominion inside the Holy Roman Empire. Scheele's father, Joachim (or Johann) Christian Scheele, was a grain dealer and brewer from a respected Pomeranian family. His mother was Margaretha Eleanore Warnekros.
Friends of Scheeles parents taught him the art of reading prescriptions and the meaning of chemical and pharmaceutical signs. Then, in 1757, at the age of fourteen, Carl was sent to Gothenburg as an apprentice pharmacist to another family friend and apothecary, Martin Andreas Bauch. Scheele retained this position for eight years. During this time he ran experiments late into the night and read the works of Nicolas Lemery, Caspar Neumann, Johann von Löwenstern-Kunckel and Georg Ernst Stahl (the champion of the phlogiston theory). Much of Scheeles later theoretical speculations were based upon Stahl.
In 1765 Scheele worked under the progressive and well-informed apothecary C. M. Kjellström in Malmö, and became acquainted with Anders Jahan Retzius who was a lecturer at the University of Lund and later a professor of chemistry at Stockholm. Scheele arrived in Stockholm  between 1767 and 1769 and  worked as a pharmacist. During this period he discovered tartaric acid and with his friend, Retzius, studied the relation of quicklime to calcium carbonate. While in the capital, he also became acquainted with figures including Abraham Bäck, Peter Jonas Bergius, Bengt Bergius and Carl Friedreich von Schultzenheim.
In the fall of 1770 Scheele became director of the laboratory of the great pharmacy of Locke, at Uppsala, about 65 km (40 mi) north of Stockholm. The laboratory supplied chemicals to Professor of Chemistry Torbern Bergman. A friendship developed between Scheele and Bergman after Scheele analyzed a reaction which Bergman and his assistant, Johan Gottlieb Gahn, could not resolve. The reaction was between melted saltpetre and acetic acid that produced a red vapor. Further study of this reaction later led to Scheeles discovery of oxygen (see "The theory of phlogiston" below). Based upon this friendship and respect, Scheele was given free use of Bergmans laboratory. Both men were profiting from their working relationship. In 1774 Scheele was nominated by Peter Jonas Bergius to be a member of the Royal Swedish Academy of Sciences and was elected 4 February 1775. In 1775 Scheele also managed for a short time a pharmacy in Köping. Between the end of 1776 and the beginning of 1777 Scheele established his own business there.
On 29 October 1777, Scheele took his seat for the first and only time at a meeting of the Academy of Sciences and on 11 November passed the examination as apothecary before the Royal Medical College, doing so with the highest honours. After his return to Köping he devoted himself, outside of his business, to scientific researches which resulted in a long series of important papers.
Isaac Asimov called him "hard-luck Scheele" because he made a number of chemical discoveries that were later credited to others.