The total head count rose to 90,300 last year from 44,500 in 2002, when the freedom of movement accord between Switzerland and the European Union went into effect.
The figures were released by the Conseil du Léman, which groups together the cantons of Geneva, Vaud and Valais with neighbouring regions in France.
Among the frontaliers, 98 percent live in France, while 72 percent work in Geneva, 25 percent in the canton of Vaud and three percent in Valais, the organization said in a news release.
The growth of frontaliers in the three Swiss cantons has averaged 7.3 percent a year, significantly higher than the 1.7 percent average annual increase in job creation for the Swiss region.
Cross-border workers accounted for 12 percent of employees in the combined area of Geneva, Vaud and Valais in 2012, up from seven percent a decade earlier.
It is widely accepted that one of the reasons for the increase in frontaliers is that Geneva has been creating jobs at a faster rate than it has been increasing the housing stock, forcing job seekers to live in neighbouring France.
Accommodation is more available, land for development is cheaper and living expenses are generally lower in the French Ain and Haute-Savoie regions than in Geneva or Vaud.
The difference in costs has been exacerbated by the high level of the Swiss franc against the euro.
But the burgeoning numbers of frontaliers has sparked a backlash in Geneva, where the populist Geneva Citizens Movement party has gained support.
The MCG, which on Sunday elected a candidate to the Geneva cantonal government (Mauro Poggia) for the first time in its eight-year history, has campaigned on a "Genevans-first" platform, arguing that frontaliers benefit at the expense of the canton's residents.