Giovanni Battista Emanuele Maria Segatini [sic] was born at Arco in Trentino, which was then part of the County of Tyrol in the Austro-Hungarian Empire. He later changed his family name by adding another "n" after the "a". He was the second child of Agostino Segatini (1802–1866) and Margherita de Giradi (1828–1865). His older brother, Lodovico, died in a fire the year Giovanni was born. During the first seven years of his life his father, who was a tradesman, traveled extensively while looking for work. Except for a six-month period in 1864 when Agostino returned to Trentino, Segantini spent his early years with his mother, who experienced severe depression due to the death of Lodovico. These years were marked by poverty, hunger and limited education due to his mothers inability to cope.
In the spring of 1865 his mother died after spending the past seven years in increasingly poor health. His father left Giovanni under the care of Irene, his second child from a previous marriage, and again traveled in search of work. He died a year later without returning home and leaving his family nothing. Without money from her father, Irene lived in extreme poverty. She was forced to spend most of her time working menial jobs while leaving Giovanni to subsist on his own.