Secchi was born in Reggio Emilia, where he studied at the Jesuit gymnasium. At the age of 16, he entered the Jesuit Order in Rome.
He continued his studies at the Roman College, and demonstrated great scientific ability. In 1839, he was appointed tutor of mathematics and physics at the College. In 1841, he became Professor of Physics at the Jesuit College in Loreto. In 1844, he began theological studies in Rome, and was ordained a priest on 12 September 1847. In 1848, due to the Roman Revolution, the Jesuits had to leave Rome. Fr. Secchi spent the next two years in the United Kingdom at Stonyhurst College, and the United States, where he taught for a time at Georgetown University in Washington, DC. He also took his doctoral examination in theology there.
During his stay in America, he met Commander Matthew Fontaine Maury, the first Director of the United States Naval Observatory in Washington. He studied with Maury and corresponded with him for many years.
He returned to Rome in 1850. On the recommendation of his late colleague Francesco de Vico, he became head of the Observatory of the College at age 32.
In 1853, under his direction, the crumbling Observatory was relocated to a new facility on top of the Sant'Ignazio Church (the chapel of the College). Secchi served as Director until his death.
His position was challenged after 1870, when the remnant of the Papal States around Rome was taken over by the Kingdom of Italy. In 1873, the College was declared property of the Italian government. When the government moved to take over the Observatory as well, Secchi protested vigorously, and threatened to leave the Observatory for one of several positions offered to him by foreign observatories. He was offered important scientific positions and political dignities by the government, but refused to pledge allegiance to the Kingdom in place of the Pope. The royal government did not dare to interfere with him, and he continued as Director.
He died in 1878 at age 59, in Rome.