The grandson of Captain Matthew Flinders, explorer of the coasts of Australia, he was born in Charlton, England. He was educated at home by his parents. Petrie's father, a surveyor, taught his son how to survey accurately, so laying the foundation for his career.
After surveying British prehistoric monuments, including Stonehenge, Petrie went to Egypt in 1880 to measure the Great Pyramid at Giza. He went on to excavate at many of the most important archaeological sites in Egypt such as Abydos and Amarna. His painstaking recording and study of artefacts set new standards in archaeology. By linking styles of pottery with periods, he developed a revolutionary method for establishing the chronology of a site.
From 1892 to 1933 Petrie was the first Edwards Professor of Egyptian Archaeology and Philology at University College, London. This chair had been funded by Amelia Edwards, who was a strong supporter of Petrie. He continued to excavate in Egypt after taking up the professorship, training many of the best archaeologists of the day. In 1913 Petrie sold his large collection of Egyptian antiquities to University College, London. It is now housed in the Petrie Museum of Egyptian Archaeology.
Petrie left Egypt for Palestine in 1926. Here he excavated a series of frontier sites between Egypt and Canaan. He died in Jerusalem.