It marks the 20 year-old's first taste of senior football.
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Hughes spent time with the Dons in preseason as a trialist.
Hughes said: “I'm delighted to get the deal finally done and I can't wait to kick on and help the team out to progress through the season.”
Director of Football Craig Cope said: “We’re delighted to add a player of Brodi’s quality into the group, he impressed in pre-season when he stepped in to help us out and we’re excited to have him join us for the season.
"I’d also like to thank Chelsea for their support with the move.”