The company's CEO Beat Grüring told newspapers of the AZ media group that 85 percent of the chain's revenues are earned in the eurozone.
Continuing to pay wages at the company's head office in francs would represent a currency risk, Grüring is quoted as saying.
Telly Weijl, with more than 780 stores in 37 countries, had considered moving its headquarters to Lörrach, Germany, where it already has a logistics centre that handles 60 percent of its goods, he said.
But most head office employees were opposed to the move, Grüring said.
While some supported the relocation “we realized that most did not want to work in Germany”.
The company was concerned about losing workers, some of whom have already quit because of fears of a move to the German city.
All employees assigned to the Basel office will be paid in euros, while existing employees there can decided whether they want to be paid in euros or Swiss francs, the SDA news agency said.
The headquarters employs 200 people.
Staff at Telly Weijl's Swiss stores will continue to be paid in Swiss francs.
The privately owned company, which markets clothes to teens and young women, employs around 3,400 people globally with annual sales of more than €500 million.
Companies in Switzerland are struggling to deal with the franc, which the Swiss National Bank has repeatedly said is significantly over-valued against the euro.
On Wednesday, the euro was trading at around 1.08 francs after dipping as low as 1.0774 francs on Tuesday.