The Blues manager, who guided Southend to promotion to Sky Bet League One with a play-off final victory over Wycombe Wanderers, had been in talks with the club over new terms for several months.
“It’s been a long process, but I’m really pleased to be staying with Blues long-term,” said Brown. “I’ve really enjoyed my time at the club.
“Hopefully we can make some more memories together not just next season but beyond that as well.”
The former Hull City and Preston North End boss has been in charge at Roots Hall since he replaced Paul Sturrock in April 2013.