26 year-old Brown, who made 15 appearances for The Shots and scored one goal, had been offered a permanent deal by Kevin Dillon, but has chosen to be reunited with Orient manager Russell Slade, who also signed the giant centre-half for Yeovil last year.
He has signed a one-year contract at Brisbane Road.
Meanwhile the MK Dons have confirmed that Dean Morgan, who has also been offered a contract at the EBB Stadium, is set to leave the Buckinghamshire based club when his contract comes to an end next month.
The 26-year-old striker joined the Dons on a month-to-month deal in September 2009 before signing a contract in January until the end of the season.
Morgan netted twice in 12 appearances for the League One side but spent the latter part of the season on loan with The Shots were he scored four times in nine league outings helping the club to the League Two play-offs.
Again - the player will nodoubt have attracted offers from other clubs so it we will have to wait and see the outcome.