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.

Media playback is not supported on this device
Muguruza beat American five-time champion Venus Williams 7-5 6-0 in Saturday's final and is expected to rise to number five in the new world rankings on Monday.
The 23-year-old is now a double Grand Slam champion, having won the French Open last year.
Martinez told Sportsweek: "She has the potential and she can win more."
Spaniard Martinez, the 1994 Wimbledon champion, added: "She is very happy with her game. She beat the world number one, Kerber, and she can go all the way."
Muguruza was ranked 15th in the world before Wimbledon but both she and Britain's Johanna Konta, who lost to Venus Williams in the semi-final, are expected to rise above former world number one Serena Williams, who is pregnant with her first child.
Muguruza beat German world number one Angelique Kerber in the last 16 and seventh seed Svetlana Kuznetsova in the quarter-finals on the way to the title.
She was beaten by Serena in the 2015 Wimbledon final, and was determined to avoid a repeat against her sister Venus.
"I didn't want to lose this time because I know the difference. I'm so happy," she said.
"I'm happy that once again I see myself winning a Grand Slam, something that is so hard to do."

The road closed for a time last week after a landslip during Storm Frank.
It closed again on Monday amid concerns about the boulder, which is about 175m above the carriageway.
The Old Military Road diversion, which was in use since 09:00, closed at 16:30. An alternative diversion via Dalmally will be in place overnight.
In a statement, roads operator Bear Scotland, said that efforts to make safe the boulder had been been "ongoing since first light this morning".
"A helicopter bringing materials to site was delayed reaching the area due to inclement weather but the specialist teams have now begun to install the anchors required to remove the boulder safely," Bear said.
"Good progress has been made and preparatory works should be completed today ready for works to make safe the boulder to take place tomorrow morning."
Bear said the "monitoring process cannot continue safely during the hours of darkness and the Old Military Road will close at 4:30pm this evening and reopen at 9:00am tomorrow".
During this time, the diversion via Dalmally and Crianlarich will be reinstated.
Overnight, the A83 will remain open from Inveraray to the B828 junction, allowing continued access to Lochgoilhead, Dunoon and the ferries to Gourock.
At the south side of the closure, access is available from Tarbet to Ardgartan.
Conor McLaughlin's late header rescued a valuable point for relegation-threatened Fleetwood at Southend.
[NEXT_CONCEPT]
New Wimbledon champion Garbine Muguruza can be the best player in the world, says her coach Conchita Martinez.
[NEXT_CONCEPT]
The A83 at the Rest and Be Thankful in Argyll has been closed overnight as efforts continue to make safe a 150 tonne boulder on the hillside.