Ranked as lowly as 190th little over five years ago, the arrival of French coach Nicolas Dupuis has transformed the perennial also-rans into a cohesive unit that is making waves in a first appearance at the continental showpiece.
The Indian Ocean islanders held Guinea to a 2-2 draw in their debut match and have gone from strength to strength in Mediterranean city Alexandria, with a 1-0 victory over Burundi followed by "the most beautiful win in Madagascar's history", a famous 2-0 defeat of three-time African champions Nigeria.
Their reward for finishing top of the group is a last-16 encounter on Sunday with the Democratic Republic of Congo, a team that thrashed Madagascar 6-1 when the sides last met in 2016.
"All teams are better on paper than us," Dupuis told AFP, pointing out that none of the players involved that day are part of the current squad.
"Everything has changed, the team is no longer the same. The players have changed and the set-up has changed. It's much more professional, the staff as well, with proper physical trainers, physiotherapists and doctors. Everything is done better and in a professional manner. It's normal that we've had a few more results."
While Dupuis, who juggles the job with his role at a French fourth-division club, has scoured the lower reaches of the game in his homeland for prospective players, Madagascar remain decidedly short on star power.
"We don't have any stars in our team. The star is the team. We have a real team of friends but also with talented players, who are very good but perhaps not stars. Players who put with one another, if we start playing well and with tactical discipline, can make a very good team."
Charles Andriamahitsinoro was the standout performer in the group phase with two goals and an assist, but the Saudi-based attacker was quick to deflect praise back towards the group.
"We did what we needed, and at a point a player stands out individually when the team needs him. That's our strength," he said.
However, the longer-term concern for Dupuis and football in Madagascar is the lack of succession planning for a team heavily reliant on aging players, such as 35-year-old captain Faneva Andriatsima and Lalaina Nomenjanahary, 33.
"I've sounded the alarm in Madagascar. There is nothing being done from a technical standpoint at the national level, there's no work in terms of youth and it's serious," said Dupuis. "I'm raising the alarm because the national team is the tree that hides the forest.
"If we don't question everything, if we don't get back to work, in two years there will be no more team and in four even less so. It would be a shame because there's a real breeding ground and it's quite an old team. My role is to sound the alarm and tell officials there are lots of things in need of change in Madagascar."
For Dupuis and his players the significance of their success in Egypt has yet to properly sink in, but they will get a taste of the fervour back home with President Andry Rajoelina chartering a 480-seater plane to take fans to Sunday's match.
"We're not too aware of what we're doing, except when we get sent photos from Madagascar where it's madness right now," says Dupuis.
"We're trying to live in the moment as best as possible because these moments are rare. It's in these rare moments when you realise that we have the best job in the world."
Named coach of Madagascar's 'Barea' in 2017, Dupuis is out of contract at the end of the tournament but his focus is purely on the task at hand.
"To beat Egypt (in the final) in front of 80,000 people would be more than a dream," he grinned. "But we have to keep our feet on the ground. We're already happy to be here and we're going to do everything to go a little bit further."