Bobola was born in 1591 into a noble family in the Sandomir Palatinate in the Province of Lesser Poland of the Crown of the Kingdom of Poland, then a constituent part of the Polish–Lithuanian Commonwealth. In 1611 he entered the Society of Jesus in Vilnius, then in the Grand Duchy of Lithuania, the other part of the Commonwealth. He subsequently professed solemn vows and was ordained in 1622, after which he served for several years as an advisor, preacher, Superior of a Jesuit residence, etc., in various places.
From 1652 Bobola also worked as a country "missionary", in various locations of Lithuania: these included Polotsk, where he was probably stationed in 1655, and also Pinsk, (both now in Belarus). On 16 May 1657, during the Khmelnytsky Uprising, he was captured in the village of Janów (now Ivanava, Belarus) by the Cossacks of Bohdan Chmielnicki and, after being subjected to a variety of tortures, killed.
In the same year, the Cossacks surprised a holy Polish Jesuit, in the town of Pinsk, and conferred on him the palm of martyrdom, on the 16th of May, 1657. Father Andrew Bobola, ...had just offered up the holy sacrifice, when a horde of Cossacks attacked the town. On beholding the barbarians, Father Bobola fell upon his knees, raised his eyes and his hands toward heaven, and, having a presentiment that his hour had arrived, exclaimed, "Lord, thy will be done!" At that moment, the Cossacks rushed upon him, stripped him of his holy habit, tied him to a tree, placed a crown upon his head, ...after which they scourged him, tore out one of his eyes, burned his body with torches, and one of the ruffians traced, with his poignard, the form of a tonsure on the head of the venerable Father, and on his back the figure of a chasuble! To do this, the executioner had to strip off the skin of the holy martyr! But this was not yet all. The fingers of the apostle had received the priestly unction. The executioner tore from them the skin, and forced needles under his nails! And during this indescribable torture, the hero prayed for his tormentors; he preached, both by word and example, until the schismatics tore out his tongue and crushed his head. Father Andrew Bobola, whom the Church declared Blessed, the 30th of October, 1853, was sixty-five years of age.
A second account states that when Bobola refused to renounce his religion, he was stripped, tied to a hedge and whipped. In mockery, the Cossacks placed a crown of twigs on his head and then dragged him to his place of execution, a butcher's shop.