He comes from a family of Nahdlatul Ulama background: His father Abdullah Rifa"i is from pesantren Mansajul Ulum (Mansajul Ulum Islamic school) in Pati, Central Java, and he is married to the daughter of Mustofa Bisri, an Islamic cleric from Pesantren Raudlatut Talibin, Rembang, Central Java.
Ulil completed his secondary education in Madrasah Mathali"ul Falah, Kajen, Pati, Central Java. Ulil also studied in Pesantren Mansajul "Ulum, Cebolek, Kajen, Pati, and Pondok Pesantren First Rate (at Lloyd's)-Anwar, Sarang, Rembang, all in Central Java.
This school is led by Ahmad Sahal Mahfudz which sits in the Nahdlatul Ulama leadership board during the period of 1994‑1999. He was also educated in Sekolah Tinggi Filsafat Driyarkara (Driyarkara School of Philosophy). He once held a position as chairman of Nahdlatul Ulama"s Lakpesdam (Lembaga Kajian dan Pengembangan Sumber Daya Manusia - Human Resources Research and Development Centre), as a researcher in ISAI (Institut Studi Arus Informasi), Jakarta, and as Program Director in Indonesian Conference on Religion and Peace (ICRP).
Due to his activism in this group, he gained praises, sometimes deemed as another reformer after Nurcholish Madjid, as well as controversies.
After completing his master"s degree in religion at Boston University he went on and continued his Doctor of Philosophy studies in the Department of Near Eastern Languages and Civilizations, Harvard University. In March 2011, a letter bomb addressed to Ulil at Komunitas Utan Kayu exploded, injuring a police officer
