He was born in February 1978 at Victoria Hospital, in the city of Kisumu in Kenya at a time when the family had fled Idi Amin's regime in Uganda.
In 1992, he returned to Uganda and was enrolled into St. Mary's College Kisubi, graduating in 1997 with a High School Diploma (A-Level Certificate).
He continued to work there after his internship, in the pediatrics department, under the supervision of Christine Ondoa, a consultant pediatrician, who later served as Health Minister and then presidential adviser.
From 2010 until 2013, Obuku served at the Institute of Human Virology at the University of Maryland School of Medicine as a technical adviser on tuberculosis control.
[3][5] Dr. Ekwaro Obuku teaches a course in Systematic Reviews as part of the MSc Clinical Trials long-distance program, at the London School of Tropical Medicine.