But now the team are contenders to be Turkish champions and upend the traditional dominance of the three Istanbul giants of Beşiktaş, Fenerbahçe, and Galatasaray.
For their critics, Başakşehir are an artificial invention, owing their success to political support with none of the heritage or culture of the other history-laden sides.
But their success is indisputable.
After finishing second in the league last season, Başakşehir remain in contention for the Süper Lig title with a team boasting international names like Gaël Clichy and Emmanuel Adebayor.
No Istanbul side other than Beşiktaş, Fenerbahçe, and Galatasaray have ever won the Süper Lig since it was created in 1959. Outside the big three, the only other winners have been Trabzonspor (six times) and Bursaspor (once).
“Başakşehir have put themselves forward and are now one of the great clubs,” said Burak Bilgili, head of the Başakşehir 1453 supporters’ club.
“Now there are four great clubs in Istanbul,” he said.
Başakşehir are “a club growing in power,” said France-born Turkish striker Mevlüt Erdinç, who joined them last summer. “We want to be among the best.”
The rise of Başakşehir to this level, in some ways, reads like a fairytale.
They were set up in 1990 and played under the unwieldy full name of the Istanbul municipality as İstanbul Büyükşehir Belediyespor (IBB), something of a tongue twister for foreigners.
They won promotion to the Süper Lig in 2007 but were then relegated in 2014 and appeared at risk of being liquidated.
But then their fortunes changed dramatically when they were bought by a consortium of businessmen reputedly close to President Recep Tayyip Erdoğan.
The result of the acquisition was a makeover for the club and a move to the new high-rise Istanbul suburb of Başakşehir, taking the new name.
A new 17,000 capacity stadium was built, named after the legendary Turkish former player and manager Fatih Terim, who ironically manages league rivals Galatasaray.
Erdoğan blessed the club’s new look when in July 2014 he donned Başakşehir colours to play in a charity game at the new stadium in which he scored an improbable three goals in just 15 minutes.
The year 2014 also saw IBB’s former manager Abdullah Avcı return from a stint as national head coach to lead the reborn side. Unlike many Turkish coaches, he has remained in his post ever since.
In 2015 and 2016 the club finished fourth and enjoyed its first taste of European competition. Now, they are up there with the leaders.
“We are competing against clubs that are 100 years old. It’s an extraordinary situation,” said Avcı.
Top international players have since made their way to Başakşehir, and the side now boasts the likes of French former Arsenal and Manchester City player Clichy and Togo striker Adebayor.
The club also scored a major coup by securing the services of Turkey’s best-known player, Arda Turan, on a loan deal from Barcelona.
Their eye for local talent was underlined when in 2016 they picked up the then-unknown Turkish winger Cengiz Ünder. After one hugely successful season, he was then sold to Roma in a deal worth 15 million euros (RM70.6 million).
But sceptics point to the patchy attendances for home matches, which rarely rise above 5,000, and a lack of passion compared to the intensity of support at the other big Istanbul clubs.
Most controversially, the club is regarded by rival fans as a government side which would have got nowhere without Erdoğan’s support.
The club’s chairman Göksel Gümüşdağ is married to the niece of Erdoğan’s wife Emine and seen as close to the Turkish president.
On a recent visit to Başakşehir, Erdoğan said that young fans of the of the team “needed to fill the stands”, adding: “If I come to a game, I don’t want to see the stands empty.”
A critical defeat by Galatasaray last month pleased not just fans of the rival team but also opponents of Erdoğan who could not resist expressing schadenfreude.
“Galatasaray 2 Recep Tayyip Erdoğan 0,” tweeted Meral Akşener, who heads the nationalist Iyi (Good) Party and is standing against Erdoğan in presidential elections.
But Bilgili sweeps away the criticism with anger.
“We began hearing this when Başakşehir started playing for the title, getting familiar with the top and threatening the big clubs,” he said.
“Let them continue to criticise us. In the end, we will be league champions,” he said.