Jagannatha Dasa Babaji was born in a small village within the modern day Tangail district of Bangladesh. His birth year cannot be pinpointed exactly with accounts from several different Gaudiya Vaishnava groups giving years from 1750 to 1800.
Jagannatha Dasa Babaji met Bhaktivinoda Thakur in 1880, and the latter subsequently accepted the former as his instructing guru (shiksha), adopting a guru disciple relationship. Jagannatha Dasa Babaji was also the initiating guru of Bhagavat Dasa Babaji and Gaurakisora Dasa Babaji; the latter of whom would become the initiating guru of Bhaktivinoda's son, Bhaktisiddhanta Sarasvati Thakura. It is told among some Gaudiya Vaishnavas that a young Bhaktisiddhanta, skilled in astronomy, created an ample Vaishnava calendar at Jagannatha Dasa Babaji's request, detailing all holidays, including the appearance and disappearance days of prominent devotees.
Jagannatha Dasa Babaji spent his last days in the areas of Vrindavan and Navadwip, where he performed bhajan and japa in worship to Radha and Krishna. A devotee named Bihari Lal would often assist the elderly sadhu. His devotion to Caitanya Mahaprabhu and instructions on Vaishnava Theology to Bhaktivinoda Thakur and Gaurakisora Dasa Babaji render him an integral part of the Gaudiya Vaishnava Guru Parampara.