Campaigners have been calling for Sister Concelia Baxla to be released during that time.
She was arrested on charges of human trafficking after one of her co-workers allegedly took money for facilitating an adoption.
After those charges were dropped, she remained in prison.
Supporters claimed her imprisonment was an attempt to harm the Church in India.
Tehmina Arora, director of religious freedom charity ADF India, said: "Nobody should be persecuted because of their faith.
"We are thankful that Sister Concelia has been granted bail after more than a year in prison pending trial.
"While others were released sooner, it seems that Sr Concelia was punished for symbolic reasons due to her faith and her position as a member of the Missionaries of Charity."
There are growing fears over the persecution of Christians in India.
More than 200 incidents of attacks on believers have been recorded so far this year.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.