"Melbourne Children's Global Health will work with 45 low-resource countries to improve child and adolescent health equity," Murdoch Children's Research Institute director Kathryn North said.
"For example, we plan to bring our new rotavirus vaccine to millions of Indonesian children, and to tackle the growing global burden of adolescent mental health."
The three organisations already have a long history of working together.
In 1973, they discovered rotavirus, a diarrhoeal disease, and showed it was responsible for hundreds of thousands of child deaths.
"The discovery enabled national and global efforts to tackle rotavirus, but each year the virus still kills over 215,000 children under five, mainly in the developing world, and it hospitalises millions," Professor North said.
"That's why MCRI have developed a new vaccine that can be given to babies just days after birth."
The virus kills 10,000 children and hospitalises 200,000 each year in Indonesia, and the new vaccine is being trialled there.
Another focus will be on tuberculosis prevention, with about a million children falling ill and more than 200,000 aged under 15 dying from it in 2017.
University of Melbourne researcher Kathryn Snow said, as a result of under reporting, the figure could be as high as three million cases.
"Our next step is to try to understand the potential for targeting preventative measures specifically at young people in countries with intense TB epidemics," Ms Snow said.
Melbourne Children's Global Health will work with partners in Australia and the Asia-Pacific region to develop models of care for prevention, detection and treatment of TB infection and disease in adolescents.
The group also believes the initiative will help the three member institutes secure research funding and strengthen their standing at international forums.
Melbourne Children's Global Health will be launched at the Royal Children's Hospital on Friday morning.