St. Pio was named after his brother, who died shortly after birth.
Padre Pio was not born Padre Pio, as Padre (“Father”) is a reference to his priesthood and Pio was the name he was given when he became a Franciscan.
His baptismal name (given at birth) was Francesco. This is the Italian form of Francis and is a common name in Italy, being the name of St. Francis of Assisi.
However, St. Pio was not named directly after St. Francis, but after a deceased brother.
In Padre Pio: The True Story, C. Bernard Ruffin explains about the older brother Padre Pio never met.
A year after Orazio and Giuseppa were married, on June 25, 1882, a son, Michele, was born, named after Gra’s father. Two years later a second boy was born, who was given the name Francesco. Some say that he was named for Saint Francis, to whom Orazio had a great devotion. Others believe that, like most of the other children, he was named for a relative, in this case one of Orazio’s uncles. This child lived only 20 days.
A few years later when Padre Pio was born, he was named Francesco:
Then on May 25, 1887, at 5:30 p.m. according to the parish register, but at 10 p.m. according to the records of the town clerk, a fourth child came into the world and was given the name of his dead brother Francesco. This was the child who would later be known as Padre Pio.
According to family tradition, when he was baptized the next day at the parish church of Saint Anna.
It’s fitting that Padre Pio was named, in an indirect way, after St. Francis, as he has become one of the best known Franciscan saints in the world.