[9] After a couple of years, Nkengasong moved to the United States Centers for Disease Control and Prevention where he worked as Chief of Virology in Abidjan.

[13][14] At the Africa CDC, Nkengasong oversees the Regional Integrated Surveillance and Laboratory Networks (RISLNET) with a focus on empowering local leadership.

[17][18] Nkengasong led Africa's response to coronavirus disease, including training a team of young responders; the African Healthcare Volunteer Workforce.

[19][20] Protecting the African population from coronavirus disease is complicated by challenges such as difficulties in testing in regions affected by conflicts and issues with social distancing in urban slums.

[21] In the preparations for the Global Health Summit hosted by the European Commission and the G20 in May 2021, Nkengasong co-chaired the event's High-Level Scientific Panel.

[26] On August 1, 2023, Secretary of State Antony Blinken chose Nkengasong to lead the newly formed Bureau of Global Health Security and Diplomacy (GHSD), focused on coordinating international responses to infectious diseases.

[26] On 23 May 2024, Nkengasong was among the guests invited to the state dinner hosted by Biden in honor of President William Ruto at the White House.