The defeat was Southend’s eighth in nine games and saw them slip to within two points of the relegation zone.
Fleetwood came close to breaking the deadlock in the 12th minute when Devante Cole headed Ashley Hunter’s left-wing free-kick against the crossbar from 12 yards.
But Town broke the deadlock in the 57th minute when a mistake from Southend skipper Anton Ferdinand resulted in substitute Paddy Madden teeing up debutante Toumani Diagouraga to fire past the advancing Shrimpers goalkeeper Mark Oxley.
Fleetwood doubled their lead in the 62nd minute when Kyle Dempsey rolled a pass into the path of Madden, who showed good strength before netting with a well-struck finish.
Southend hit back in the 86th minute with midfielder Michael Kightly scoring a deflected effort from 20 yards but it was not enough to prevent Fleetwood securing a fourth away win in succession.
England manager Gareth Southgate has claimed that the country needs to boot racism out of its own football before criticising World Cup hosts Russia.
Newcastle have been linked with a shock move for former Sunderland goalkeeper Simon Mignolet during the summer.