Udekwu returned to Nigeria in 1965 as paediatric thoracic and cardiovascular surgeon at the University College Hospital of the University of Ibadan. He left Ibadan to Enugu at the outbreak of hostilities that marked the beginning of the Nigeria civil war. He served as a Military Surgeon and Head of the Biafran teaching hospital in various locations including Enugu and Emekukwu during the war. He was also the secretary to the Biafra Relief and Rehabilitation Association during the war. Udekwu was later rated Distinguished Professor and Head of Department of Surgery of the University of Nigeria, Teaching Hospital (UNTH) and was the administrative head of the Enugu Campus of the University. Professor Udekwu is credited with building up the Department of Surgery of the University of Nigeria. Despite several unsuccessful attempts at sourcing funds to establish a modern surgical department from many organisations in the United States, United Kingdom, Scandinavia and through church aid, he was able to source funds from the Enugu campus by the contributions of individual Nigerians to build the operating theater and buy the equipment needed to establish facilities for open heart surgery in Nigeria. He was one of the pioneers that established cardiac surgery in Nigeria. Professor Udekwu led the team of surgeons that performed the first successful open heart surgery in Nigeria in 1974 which was the first of its kind in black Africa. Also in the team of surgeons that performed this landmark operation were Professor Sir Magdi Yacoub, Professors Anyanwu C.H., Nwafor D.C., the anaesthetist Dr. Shreeniwas Jawalekar and others. This was followed by a series of six further open heart surgeries under Udekwu at the University of Nigeria Teaching Hospital Enugu (UNTH) between 1974 and 1980.