Preventing pregnant girls and adolescent mothers from attending school denies them access to education and keeps many trapped in a cycle of poverty, the charity said, adding that the ban largely affected girls from impoverished families.
This, in turn, exposes them to violations including child and forced marriage, female genital mutilation, and sexual and labour exploitation, it added.
Tanzania has one of the world's highest teen pregnancy rates. About 27% of girls aged 15-19 are pregnant, the United Nations says, as widespread sexual abuse and poverty forces many girls to exchange sex for school fees, food and shelter.
The east African nation's policy of expelling pregnant girls from primary and secondary school dates back to 1961, but expulsions have increased in recent years - largely due to public endorsement by President John Magufuli, campaigners said.
Magufuli, who was re-elected for a second term in October, has voiced support for the ban in the past, saying the "immoral behaviour" of pregnant girls should not be allowed to permeate the country's schools.
Gabrielle, 17, whose name has been changed to protect her identity, was expelled from school when she got pregnant two years ago.
"Life was hard for my siblings and I growing up. My mother struggled to make ends meet and we would often go to bed without a meal," she was quoted as saying by Equality Now.
"When I was 15, I met a man who was about 26-years old. He would buy me many different things including personal effects and when he started demanding for sex, I gave in. I got pregnant in the same year."
There is no accurate data on the number of girls in Tanzania who have been affected by the ban, but women's rights groups estimate that thousands of female students are forced out of education every year.