Prof Ndung'u, who was Dr Njoroge's predecessor, has replaced Ukur Yatani as the head of the Exchequer.
Dr Njoroge is in charge of the country's monetary policy. And among his roles is ensuring that there is price stability in the economy by using such tools as the Central Bank Rate (CBR), CBK's benchmark lending rate, to increase or reduce interest rates charged by commercial banks.
Prof Ndung'u, on the other hand, will be in charge of the fiscal policy - taxation and government spending.
Economists agree that there is a need for a symbiotic relationship between CBK and the National Treasury.
After all, CBK is also the banker and fiscal agent for the government.
But as has been the case in several countries amid recession fears, the fiscal and monetary policies have largely been at odds with each other.
In Kenya, for example, the new government of President William Ruto has signalled that it wants cheap money for the hustlers - mama mboga (greengrocers), boda boda operators and jua Kali artisans. However, following a surge in the prices of goods and services in the economy, CBK's Monetary Policy Committee has been tightening the supply of money by increasing the CBR.
This has, in turn, seen banks increase their interest rates.
This is likely to accentuate the differences between Dr Njoroge and Prof Ndung'u. From the surface, it looks like the two are cut from the same cloth.
They are agemates. Dr Njoroge is 61 years old, while Prof Ndung'u is 62. They both went to the University of Nairobi, where they studied economics.
But as the World War II British Prime Minister Winston Churchill once said, if you put two economists in a room, you get two opinions, unless one of them is Lord Keynes, in which case you get three opinions.
But their personalities are different, and so are their worldviews.
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If banks hate Dr Njoroge, digital lenders loathe him.
Most of them will never forgive him after he made them lose hundreds of millions of shillings after he denied them access to the Central Reference Bureaus (CRBs), a move that saw many borrowers refuse to pay their loans.
Some accuse Dr Njoroge of overregulation. This overregulation, they fear, is crippling innovation. Strathmore University Academic and Research Director, Dr Jim Mcfie, said over-regulation will kill the industry that is operating at this critical time where there is full transformation to technology.
"You should not just keep people out because of anti-money laundering and not financing crime. This can happen very few times in our history in Kenya. All the legislation is there, so let us be open to innovation," said Mr Mcfie.
On the other end, Prof Ndung'u has sought to portray himself as pro-innovation, particularly when he was the CBK boss. He boasted of how he mid-wifed M-Pesa, a revolutionary mobile money transfer service owned by Safaricom, at a time when there were grumbles against it, including from banks.
If Dr Njoroge, who worked at the International Monetary Fund (IMF) before, is for stricter regulation, Prof Ndung'u comes off as one who is for fewer regulations. The latter is somewhat a market fundamentalist, who believes in minimal intervention.
His hands-off approach, some critics say, saw him preside over the highest increase in prices of basic commodities in the economy in 2011 even as the shilling slumped against the dollar.
A poll by Reuters ranked him (Prof Ndung'u) as the worst CBK Governor in sub-Saharan Africa. The plunge in the shilling and hike in prices saw MPs attempt to sack him through a censure motion. He survived narrowly.
But, his non-interventionist approach might also have contributed to the double-digit growth in credit to the private sector. But interest rates, during his time, never came down leading to the controversial decision by the National Assembly to introduce interest rate controls in 2016.
Some also reckon Prof Ndung'u was cosy with banks. His name was dragged into the Imperial Bank saga, with his wife said to have received gifts from the lender's former managing director Abdulmalek Janmohamed, the court was told.
Prof Ndung'u, however, dismissed the claims as false.
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