After a goalless first half, Fleetwood went in front when Bobby Grant's superb long-range effort flew beyond Shrimpers goalkeeper Daniel Bentley.
Adam Barrett's header and Jack Payne's 18-yard strike looked to have sealed a Southend comeback, but McLaughlin's close-range header levelled the scores.
The draw moved the Cod Army one point clear of the bottom four in League One.
But any chance of a late play-off push now looks to be over for Phil Brown's Southend, who drop to 11th, nine points behind sixth-placed Walsall.
Conor McLaughlin's late header rescued a valuable point for relegation-threatened Fleetwood at Southend.