The 54-year-old faces Hull for the first time since his departure from the KC Stadium in 2010 when the Premier League side travel to Essex for the sold-out fourth-round tie.
Brown took Hull into the top flight for the first time in their history during his four years in charge and after a short spell at Preston he now has the Shrimpers on a real crest of a wave.
They head into this cup tie having lost just once in their last 15 games, a run which has lifted them to within three points of League Two leaders Scunthorpe.
And having claimed the scalp of Championship side Millwall in round three, 10,000 supporters will squeeze into Roots Hall for the tussle with the Tigers.
"The atmosphere at Roots Hall won't be the same as any league game. Games in the FA Cup create a special feel around the place," Brown told his club's website.
"We experienced some of that magic against Millwall but if we can do it again against Hull City it will be brilliant.
"When I first came to the club I said I wanted to see a packed Roots Hall with not a seat spare. That's going to be the case on Saturday afternoon and it should make for an unbelievable cup tie.
"It should be magnificent."
Brown was quick to shrug off suggestions of resentment as he prepares to be reacquainted with the Hull faithful.
"I went back for a fans' presentation where they wanted to honour me which was nice," he told BBC Essex. "So I don't have any axes to grind with any of the fans.
"I don't think there are any problems as far as the Hull fans are concerned. I don't have any problems with Steve Bruce or the owners, because it was a different owner at the time."
The owner is not the only change since Brown's departure from Hull, with Paul McShane the only survivor from his days still in the squad.
Current Hull boss Bruce made nine changes as his team knocked out Middlesbrough in the third round, and with star playmaker Tom Huddlestone suspended and new strikers Nikica Jelavic and Shane Long cup-tied the visitors will not be at full strength for their trip.
In-form Southend midfielder Ryan Leonard, heading into the clash looking for his fifth goal of January, hopes the hosts can make the most of any squad rotation from Bruce.
"I expect they will make a few changes and hopefully we can take advantage of that," Leonard said. "Whatever team they put out it will still be a very strong side, but we are a team full of confidence thanks to our recent results.
"We will have to be at our very best if we are going to upset the odds, and hope they aren't at their best. But we know anything can happen in this competition."