Hinkie, who served as executive vice president of basketball operations in Houston, replaces interim GM Tony DiLeo, whose contract reportedly wasn't renewed.
In Houston, Hinkie was responsible for the Rockets' much-praised basketball data analytic operations.
His first job will be to find a replacement for former Coach Doug Collins, who resigned after three seasons.
"Sam is a proven innovator and holds values that align with those of our ownership group," Sixers managing owner Josh Harris said. "Sam's experience, his judgment and his analytical approach make us confident that he is the right leader to build a foundation for long-term success -- with the goal of ultimately contending for a championship -- here in Philadelphia."
The injury-riddled Sixers struggled to a 34-48 mark this past season.