Gillingham came from behind to beat Southend United 3-1 for the second time in four days.

Loan striker Jay Emmanuel-Thomas came off the bench and delivered a masterclass, scoring twice, to secure Gills a place in round two of the League Cup.

It wasn’t all good news for the Gills, however, as they suffered more injury woes.

Gillingham were a goal behind at the break, through Stephen McLaughlin, but more of a concern was injuries to Max Ehmer and Bradley Dack.

Ehmer was stretchered off after appearing to have been knocked out in a collision with Southend’s Luke O’Neill. Dack lasted less than half an hour when he hobbled off clutching his knee following an innocuous looking challenge in the middle of the park.

But goals from Cody McDonald and two from substitute Emmanuel-Thomas turned the first round tie on its head.

Gills boss Justin Edinburgh made four changes to his team, resting Emmanuel Osadebe, Jay Emmanuel-Thomas, Deji Oshilaja and Mark Byrne from the side which beat Southend 3-1 at the weekend.

Joe Quigley came in to partner Cody McDonald upfront, Billy Knott and Jake Hessenthaler played in midfield while newly signed West Ham loanee Josh Pask played alongside Ehmer in central defence.

Within 30 minutes the starting XI was disrupted by injuries as Ehmer and Dack both went off injured.

Shortly after Dack had limped off Southend took the lead. A knock-down from Jakub Sokolik was pounced upon by Stephen McLaughlin and Gills keeper Stuart Nelson was unable to get two hands on the ball to prevent the ball crossing the line.

Prior to that neither keeper has been properly tested.

Before the break the Gills came close with a header from McDonald, going just wide off a Josh Wright cross, while Jake Hessenthaler also shot wide.

The early second half chances went Southend’s way. Simon Cox put an effort wide of the post and Ben Coker’s wicked cross from the left just needed a touch.

McDonald levelled the scores with 56 minutes gone. Knott’s corner was cleared back to him and when the cross came back in, Southend failed to clear their lines allowing the Gills striker to smash the loose ball home.

Emmanuel-Thomas caused problems when he came on. Paul Konchesky ran onto his ball through the defence but was just offside. Moments later the striker’s cross almost found Hessenthaler at the back post but Ben Coker made a vital interception.

The Gills took the on 76 minutes when McDonald laid the ball off to Emmanuel-Thomas, he turned on the edge of the box and fired low past keeper Mark Oxley.

Emmanuel-Thomas continued to enjoy himself, taking on Coker before shooting narrowly wide with six minutes left. He then made it 3-1, dancing past the keeper from a Nelson clearance before rifling the ball home with two minutes left.

The draw for round two takes place on Wednesday night on Sky Sports 1.

Gillingham: Nelson, Jackson, Konchesky, Ehmer (Oshilaja 17mins), Pask, Knott, Hessenthaler, Wright, Dack (Osadebe 30mins), Quigley (Emmanuel-Thomas 63mins), McDonald. Subs not used: Hadler, Oldaker, Byrne, Donnelly.

Southend: Oxley, Demetriou, White, Sokolik, Coker, O'Neill, Leonard, King (Williams 87mins), McLaughlin (McGlashan 79mins), Mooney (Bridge 79mins), Cox. Subs not used: Smith, Thompson, Barrett, Atkinson.

Attendance: 3,175 (359 away)