Originally, the obelisk was created by Pharaoh Thutmose III for himself and another for his father, but neither were completed before his death. Thutmose III's grandson, Thutmose IV finished the obelisks and had them erected to the east of the great temple of Amun in Karnak. When it was completed, the obelisk now known as the Lateran Obelisk stood at 32m which was the tallest one in Egypt. Both it and the other obelisk, known as the Obelisk of Theodosius, were brought to Alexandria over the Nile by an obelisk ship in the early 4th century by Constantius II. He intended to bring both obelisks to Constantinople, the new capital for the Roman Empire. The Lateran Obelisk never made it.
After the obelisk remained in Alexandria for a few decades, Constantius II had the Lateran obelisk shipped to Rome when he made his only visit there in 357. It was erected near the Egyptian obelisk called the Flaminio, which had stood since 10 BC where it was installed by Augustus to decorate the spina of the Circus Maximus. There they both remained, until after the fall of the Western Roman Empire in the 5th century the Circus Maximus was abandoned and they eventually broke or were taken down. They were eventually buried by mud and detritus carried by a small stream over time. First person accounts have the original base of the monument still in the Circus Maximus as late as 1589. It contained a narrative of Constantius' transport, raising, and dedication of "his father's" obelisk inscribed on its four sides as a long epigram.
Though pieces of the obelisk had been found in the 14th and 15th centuries, serious excavation was only made possible under Pope Sixtus V. The three pieces of the Lateran obelisk were dug up in 1587, and after being restored by architect Domenico Fontana, the obelisk was re-erected approximately shorter. When it was erected near the Lateran Palace and basilica of St. John Lateran on 9 August 1588, it became the last ancient Egyptian obelisk to be erected in Rome. Its location was formerly the spot where the equestrian statue of Marcus Aurelius stood until 1538, when it was relocated to decorate the Piazza del Campidoglio on Capitoline Hill. The obelisk was topped with a cross and the pedestal was decorated with inscriptions explaining its Egyptian history and its travels to Alexandria and Rome, mentioning the baptism of Constantine the Great.