Kagame swept to a landslide victory in a presidential election last year, securing a third term in office and extending his 17 years in power.
Late on Friday, he promoted state minister of finance Ndagijimana to replace Claver Gatete as finance minister, the office of the presidency said.
Gatete, a previous central bank head credited with overseeing a period of relative monetary stability, was named minister for infrastructure.
The economy has been rebuilt with a focus on technology, mining, tourism and agriculture following the 1994 genocide of 800,000 ethnic Tutsis and politically moderate Hutus.
Growth rates have averaged 5-6 percent over the last decade. This year, the International Monetary Fund expects its economy to expand by 7.2 percent.