Nilar Thein is from Yangon, Burma. She and her future husband, Kyaw Min Yu (better known as "Ko Jimmy"), participated in 1988's pro-democracy 8888 Uprising, opposing the continued rule of the military dictatorship State Law and Order Restoration Council (SLORC). In 1990, she was imprisoned for two months for her participation in protests. In December 1996, she was arrested for organizing protests and sentenced to ten years imprisonment, which she served at Thayawaddy prison. She reported being abused and sexually harassed by prison staff during this sentence, stating that "under the prison chief, U Win Myint, prisoners sentenced for rape were kept next to the women’s building... Prison staff and these prisoners would come and peep at us while we took our baths." She was released in 2003. In 2005, she married Kyaw Min Yu. At around the same time, she joined the newly formed 88 Generation Students Group.
In August 2007, anti-government protests (popularly known as the "Saffron Revolution" for the prominent involvement of Buddhist monks) broke out in Yangon in response to increasing fuel and commodity prices. As a part of the protests, Nilar Thein organized a march of roughly 500 people to protest government policies. When police began seeking the organizers of the protest, Nilar Thein went into hiding. Her husband had already been arrested on the night of 21 August and sent to Insein Prison.
In May, Nilar Thein had given birth to a baby girl, Phyu Nay Kyi Min Yu, and when hiding with the infant became too difficult, she left the child with in-laws. She then evaded capture for a little more than a year, changing locations and cell phone numbers frequently to avoid detection; she told a reporter that at one point in this period she escaped arrest in a rickshaw taxi. In March 2008, People in Need awarded Nilar Thein, along with political prisoners Su Su Nway and Phyu Phyu Thin, the Homo Homini Award. On 19 June 2008, Nilar Thein published an editorial in the English-language Thai newspaper The Nation, protesting the Burmese government's treatment of women and children. In it, she asks, "When the government itself is the abuser of human rights and the perpetrator of rape and other forms of gender-based violence, who will protect the victims? Who will end their tragedy? Who will secure the joyful reunion of mothers with their children?"
On 10 September 2008, Nilar Thein was arrested on her way to visit the mother of another political prisoner, Ant Bwe Kyaw, in Yangon. On 11 November, she and her husband were convicted along with fellow 88 Generation Students Group members Htay Kywe, Mie Mie, and ten other activists on four counts of "illegally using electronic media" and one count of "forming an illegal organization". At that time, all fourteen were serving 65-year sentences at Thayet prison.
In January 2009, her family heard secondhand information that she had developed a peptic ulcer and were concerned that her health might be deteriorating. In December 2010, Nilar Thein's family reported that prison officials had barred them from seeing her, even to bring Nilar Thein's child for a visit. Nilar Thein responded with a hunger strike.
Nilar Thein and Ko Jimmy were released on 13 January 2012 in a mass presidential pardon of political prisoners. Speaking from outside the prison on the day of her release, she told The Irrawaddy that "I’m happy, and I will be very happy to see my family. We will get involved in democratic reform with Auntie [Aung San Suu Kyi]."