Following his master’s degree, he worked in Nairobi as a planning officer at the Kenyan Ministry of Planning from October 1985 until August 1987. Following his PhD studies, he worked as an economist at the Kenyan Ministry of Finance from March 1993 until December 1994.
From April 1995 until October 2005, he worked at the International Monetary Fund (IMF) in Washington, D. C., first as an economist and later as a senior economist. From November 2005 until December 2006, he served as the IMF mission chief for Dominica. He then served as the deputy division chief, Finance Department, at the IMF, from December 2006 until December 2012, based in Washington, D. C. from December 2012 until June 2015, he served as advisor to the deputy managing director of the IMF.
He was nominated to be the governor of the Central Bank of Kenya by Uhuru Kenyatta, the president of Kenya, on 2 June 2015. After vetting by the parliamentary committee on Finance, Trade and Planning on 17 June 2015, he was approved by the parliament of Kenya on 18 June 2015. He assumed office effective 19 June 2015.
On 13 October 2015 the Central Bank of Kenya under his leadership placed Imperial Bank into receivership.
In November 2018, United Nations Secretary General António Guterres appointed Njoroge to the United Nations’ Task Force on Digital Financing of Sustainable Development Goals, co-chaired by Maria Ramos and Achim Steiner.