During the one-year study, the craft will be blasted with the equivalent of more than 100 million dental x-rays, meaning its most sensitive instruments had to be protected within a titanium vault.
Scientists hope Juno will reveal water levels in Jupiter's atmosphere, the nature of its magnetic fields and deep structure, and the make-up of its composition, temperature and cloud motions.
While the planet has been studied for hundreds of years, we still have no absolute answer to how it formed, whether it has a solid core, how much oxygen it holds, or what its poles look like.
Like the sun, Jupiter is made up of mostly hydrogen and helium, meaning it must have developed early, capturing most of the material left from the formation of our sun.
By measuring the amount of water and the mass of Jupiter's solid core, scientists hope to decide which theory about the planet's origin is correct.
"We know much about what it looks like from the outside, but know almost nothing about what's on the inside - only what's been inferred by experts," said Dr Grant Christie, an astronomer at Auckland's Stardome Observatory. "Now that we've found lots of Jupiter-mass planets orbiting other stars, there are a number of competing theories as to how such big planets formed, why, and what their influence has been on the subsequent formation of solar systems."
Jupiter had been fundamental to the evolution of our solar system, weighing twice as much as all of the other planets, asteroids and comets within it combined. "It's probably why we are here."
After about a year of study, Juno will be sent into Jupiter's atmosphere, where it will burn up like a meteor, but Dr Christie suspects it won't be the last time we venture into the planet's neighbourhood.
Exobiologists believe Europa, the sixth-closest moon of Jupiter, is one of the hot-spots in the solar system for finding extra-terrestrial life.
