Peter Taylor admitted to having flashbacks to Peterborough’s last visit as the Gills entered injury time on Tuesday night.
Last December the Gills led Peterborough 2-1 before conceding an equalising goal in the eighth minute of injury time.
Two goals from Cody McDonald put them 2-1 up again but this time his side saw the game out.
He said: “When I saw the five minutes go up I must admit I did have thoughts but we are pleased.
“We are pleased, that as much as Peterborough looked a very good football team, there weren’t a lot of clear-cut chances, there were more in the first than the second half.
“It feels terrific that we have got three points against a very good team. We know we have to work very hard for anything you get at this level so when you beat one of the top sides in the division it’s a good feeling.”
Peterborough came into the game having won their opening three away games.
And they started Tuesday’s game well.
“For 10-15 minutes they were very good,” said the Gills boss.
“I thought maybe we didn’t believe enough in that period. Of course, a goal was going to change certain things but all of a sudden I felt we believed a little bit more and we got better.
“Of course you are always going to see good passing moves from Peterborough, because they are good at it. If you go too high to get it back off them, they could open you up too much, so we decided to let them have it in certain areas.”
Gills’ winning goal came in the 86th minute and Peterborough were unable to pose too many threats after that.
“I am pleased they stayed together as a group, that’s the most important thing,” Taylor said.
“There are teams in this division that are better than us and we have to work extremely hard as a unit to get anything out of games. The boys did that.
“There were times where they passed around us and we couldn’t get near them but we hung in there and the boys did their job.
“Sometimes their brains got a touch tired and we got out of position on a few occasions but overall for 90 minutes they stuck at their task.”