The Cod Army raced into a two-goal lead through Junior Brown and Alan Goodall but a Charlie Lee effort before the break reduced the arrears and substitute Myles Weston rescued a point for Gillingham. Brown thought he had given Fleetwood all three points late on, only to see his effort ruled out for offside.
But despite dropping points, Allen hailed his comeback kings.
"It's another game gone, it's another week gone," said Allen. "We've said all along this season lasts for 10 months, and we're still five points clear. Every point is a good point.
"I didn't expect us to be 2-0 down. I thought the players were doing okay, and we certainly weren't two goals worse than them. I suppose throughout the season, these days are going to happen.
"When were 2-0 down, we remained pretty calm. We weren't banging our heads against the wall or asking for the Nurofen. We upped the ante after half-time and they stepped up and performed for the crowd. That second half was up there with the best we've had all season.
"The players have got to get used to being top of the league. Everyone outside of the club talks about it all the time. For all of us, you have to cope with that and step up."
Fleetwood manager Graham Alexander. who has drawn his first two games at the helm, said: "When you come to Gillingham, it's going to be tough. I thought we were fantastic in the first half, we kept them at arm's length, we didn't let them get near the box and I thought we deserved to be in front.
"When you're 2-0 up, you've put yourself in the driving seat and you want to take all three points. Unfortunately they got a goal just before half-time and then second half we knew we were going to be put under pressure.
"They worked us, they brought on two or three big lads, but for the majority of the 90 minutes, I thought we stood up to it. I thought we matched Gillingham for tempo. We know they're a fit side and we matched that and played our own stuff as well."