The nun became pregnant after she was raped by a man carrying out repairs at the convent.
She alleges that, when her fellow sisters found out about her pregnancy, they pressured her to leave the convent and the Church.
Her lawyer says the sisters blamed her for having been raped.
She is suing the Archbishopric of Santiago and the Order of St Clare.
The Auxiliary Bishop of Santiago, Rt Rev Jorge Concha, said that the nun had left the convent "voluntarily" and the Archbishopric had only found out about the rape and subsequent events on 27 March.
The nun told Chilean TV that she had joined the order in 2002 when she was 20 years old.
She said she lived inside a convent in the capital Santiago, with very little contact with the outside world.
But in 2012, a group of men was allowed into the convent to carry out some repairs. They lived and slept in the convent for the duration of the renovations and the nun was assigned to provide them with food.
One of them raped her, a fact she kept secret from her fellow sisters "out of fear and shame, because a sense of shame came over me and didn't let me express myself," she told 24 Horas.
Three months on, the sisters found out that she was pregnant.
"[I got] zero support, they told me I was to blame, that I did it on purpose," the nun told Chilean TV.
"I told them I was innocent, but my fellow sisters were very cruel to me."
She alleges that they pressured her to leave the convent and the Church.
"They wanted me to hand over my habit, but I wasn't going to do that," she said.
While she did eventually leave the convent she says she refused to sign any papers saying she would leave the Church.
She says she sought shelter with a friend and after giving birth, put her child up for adoption.
In 2015, her rapist was found guilty and sentenced to five years in jail.
Her lawyer says it is time for the Archbishopric of Santiago "to own up to its responsibility" in the case.
"She is a nun living in a convent who was raped and instead of being protected she was blamed for what happened," her lawyer Camila Maturana said.
"In a convent, where nuns are kept separate from worldly life, men shouldn't stay overnight," Ms Maturana said.
"All religious institutions in a diocese fall under the aegis of a bishop, in this case it's the Archbishop of Santiago," she added, to explain the decision to sue the Archbishopric as well as the Order of St Clare.
The nun said she felt "abandoned by my only family and my Church, which I have always defended like a lioness".
Bishop Concha said the Archbishopric had been unaware of the nun's plight until 27 March.
A nun in Chile is suing the religious order she belonged to after its members pressured her to leave her convent over her pregnancy.