Golenishchev, the son of a well-to-do merchant, was educated at the Saint Petersburg University. In 1884–85 he organized and financed excavations in Wadi Hammamat, followed by the research at Tell el-Maskhuta in 1888–89. In the course of the following two decades he travelled to Egypt more than sixty times and brought back an enormous collection of more than 6,000 ancient Egyptian antiquities, including such priceless relics as the Moscow Mathematical Papyrus, the Story of Wenamun, and various Fayum portraits. He also published the so-called Hermitage papyri, including the Prophecy of Neferti, now stored in the Hermitage Museum.
Having sold his collection to the Moscow Museum of Fine Arts in 1909, Golenishchev settled in Egypt. Following the Russian Revolution of 1917, he never returned to Russia, residing in Nice and Cairo. In Egypt, he established and held the chair in Egyptology at the University of Cairo from 1924 to 1929. He was also employed by the Egyptian Museum in Cairo, where he catalogued hieratic papyri. Golenishchev died in Nice aged 90. Some of his papers are in the Griffith Institute, Oxford.