Women in Silicon Valley own less than half the startup equity that men own, according to a new study.

CARTA, a company that manages equity and ownership, found female startup employees own just 47 cents for every dollar their male counterparts own. The disparity is even greater for female founders, who hold just 39 cents of equity to the dollar.

The study shines a light on an early-stage disparity that could cripple women's voting power and piece of the proverbial pie.

Women make up 35 percent of startup equity-holding employees, but hold only 20 percent of employee equity, CARTA says. The company partnered with an investment group called #Angels and reviewed more than 6,000 startup capitalization tables.

Greater equity in existing startups can fuel future holdings in burgeoning startups, keeping men firmly at the table.

—CNBC's Julia Boorstin contributed to this report.