Happy Mkali holds a bachelor's degree in biotechnology and laboratory sciences from Sokoine University of Agriculture (Morogoro, Tanzania) and a master's degree in molecular biology from Vrije Universiteit Brussel (Brussels, Belgium), which she earned in 2016. She continued her work with the Ifakara Health Institute (IHI) in Tanzania on a global surveillance project for emerging zoonotic viruses.

In 2020, she joined the Ph.D. program in biomedical sciences (Global Health track) at the University of Geneva under the supervision of Professor Isabella Eckerle. Her doctoral project focuses on intelligent surveillance and early detection of epidemics based on an electronic clinical decision support algorithm used for the management of sick children in Tanzania.