Fabritius was born in the ten-year old Beemster polder, as the son of a schoolteacher. Initially he worked as a carpenter (Latin Fabritius). In the early 1640s he studied at Rembrandt's studio in Amsterdam, along with his brother Barent Fabritius. In the early 1650s he moved to Delft, and joined the Delft painters' guild in 1652. He died young, caught in the explosion of the Delft gunpowder magazine on October 12, 1654, which destroyed a quarter of the city, along with his studio and many of his paintings. Only about a dozen paintings have survived. According to Houbraken, his student Mattias Spoors and the church deacon Simon Decker died with him, since they were working on a painting together at the time. In a poem written by Arnold Bon to his memory, he is called Karel Faber.
Of all Rembrandt's pupils, Fabritius was the only one to develop his own artistic style. A typical Rembrandt portrait would have a plain dark background with the subject defined by spotlighting. In contrast, Fabritius' portraits feature delicately lit subjects against light-coloured, textured backgrounds. Moving away from the Renaissance focus on iconography, Fabritius became interested in the technical aspects of painting. He used cool colour harmonies to create shape in a luminous style of painting.
Fabritius was also interested in complex spatial effects, as can be seen in the exaggerated perspective of A View in Delft, with a Musical Instrument Seller's Stall (1652). He also showed excellent control of a heavily loaded brush, as in The Goldfinch (1654). All these qualities appear in the work of Delft's most famous painters, Vermeer and De Hooch; it is likely that Fabritius was a strong influence on them.