After graduating, Mbacké moved to Bamako, where he started his career as a demographic researcher.[6] He worked at the Unité Socio-Economique et de Démographie (USED).[6] Here he was involved with the first Senegalese census.[1] Mbacké joined the International Union for the Scientific Study of Population (IUSSP) in 1989.[5][6]
Mbacké advocated for the expansion of USED, and soon it became the Centre d'Études et de Recherche sur la Population pour le Développement (CERPOD). He was eventually appointed Head of the Training Division at the Sahel Population and Development Research Center.
In 1992 Mbacké left CERPOD to create a Rockefeller Foundation African population science office in Nairobi.[6] He led a series of research projects that connect international foundations with researchers in Africa. He was appointed the Rockefeller Foundation Representative for Africa in 1999 and Director of Africa Programs in 2000.[1] He was awarded the Rockefeller Foundation Outstanding Achievement Award in 2003.[1] In 2003 he moved to the Rockefeller Foundation headquarters in New York City, where was made Vice President for Regional Planning.[3]
He joined the population program at the William and Flora Hewlett Foundation in 2006 as a senior advisor.[3] In this capacity he supports the training of African population scientists.[3] Mbacké has argued that African leadership has to make sustainable health policies.[7] He served on the council of the IUSSP between 2010 and 2013.[6]
He joined Center for Research on Applied Economics and Finance at the Université de Thiès in 2015, where he uses the National Transfer Accounts approach to study demographic change and economic growth.[2] That year he was named the IUSSP laureate.[6][8] The Hewlett Foundation described the impact of Mbacké's work,
"Almost every African demographer, and many population scientists from other regions, can trace a pivotal moment in their own careers to advice, support, ideas, and constructive critique offered by Cheikh Mbacké."[9]
Mbacké is Chair of the Board of Directors of Tostan, an organisation in Africa that looks to develop rural communities in Africa.[10] He serves on the Board of Directors of the African Institute for Development Policy.[11] He is a member of the World Health Organization (WHO) African advisory committee on health research and development.[12]
Mbacké was elected a foreign associate of the National Academy of Sciences (NAS) in 2018.[2]