She graduated from the law school at the University of Nairobi and began an unchallenging job at the Attorney general's office. She left there to join Lee Muthoga and Associates where she felt purposed. She started to build up a private practice and a reputation as an advocate in company law.
She is married to another lawyer with whom she has two children.
She started her own law company and she became an advocate for women's rights. She saw that the Kenyan police turned a blind eye to abuse cases where the woman and family relied on the man's income. She realised that the culture was at fault. She organised training sessions for the police to inform their actions. Thongori spent five years leading an association of women lawyers. She was recognised by the Institute for Inclusive Security and  Thongori's highest profile case was when she won a case against the Kenyan government when they failed to deliver 30% representation for women.
In 2015 she was chosen to be one of 21 women who met for a conference at Harvard University Kennedy School of Government funded by Hunt Alternatives. The group included Fauzia Nasreen from Pakistan and Olufunke Baruwa, Esther Ibanga, Hafsat Abiola and Ayisha Osori from Nigeria.
- Faith Wambura Ngunjiri (23 February 2010). Women's Spiritual Leadership in Africa: Tempered Radicals and Critical Servant Leaders. SUNY Press. pp. 79–82. ISBN 978-1-4384-2978-6.
- Judy Thongori: I derive energy from my husband, 2010, Standard Media, Retrieved 7 February 2016
- Judy Thongory, InclusiveSecurity.org, Retrieved 7 February 2016
- 10 Kenyan women Obama should know, InclusiveSecurity.org, Retrieved 7 February 2016
- 17 women changing the world, Jan 2015, InclusiveSecurity, Retrieved 8 February 2016