The country, where more that half the population live in poverty, has about 4 million births every year spread out across 6,000 islands.
The Global Alliance for Vaccines and Immunisation (GAVI) works with UNICEF, AUSAID, the Indonesian Government and the Bill and Melinda Gate's Foundation with the goal of immunising every baby in Indonesia.
The GAVI Alliance convinced the Indonesian government to commit to continuing the program into the future.
The jab given to children is called a pentavalent, which protects against diphtheria, pertussis, tetanus, hepatitis and influenza.
In a small west Java village, 38-year-old Sri has brought her tiny son, Faizal, to be vaccinated.
"I feel more at ease because he's been protected against certain diseases," she said.
"It's really good for children, and it's really helpful for mothers as well."
GAVI Alliance chief executive Helen Evans said immunisation is the "best investment".
"In Australia, if our kid gets sick we rush off to accident and emergency [and] the children get put on drips and they get antibiotics. Here, that just isn't available and children die, so it's very significant," she said.
"Indonesia has a huge birth cohort, every year 4 million kids are born and immunisation is probably about the best investment you can make in children's health in terms of giving them a good start in life."
Nicole Bates works for the Bill and Melinda Gates Foundation, which has already donated $2.5 billion to the GAVI Alliance, and says vaccination not only helps to protect against poor health, it also helps lower poverty.
"If you have a healthy child, your child can learn, he or she can go to school and can be a productive citizen in the future," she said.
"If you have a sick child you lose days at work, so your family is at risk."
However, Indonesia still has huge child health challenges with about 20 per cent of the children are malnourished and underweight, while nearly 40 per cent suffer from stunted growth.