The results were more dismal for cyber charter schools: Students at 100 percent of them performed "significantly worse" than their counterparts in district schools.
The report does not identify the schools. Of the state's 135 charter schools, 74 are in the Philadelphia. The state also has 12 cyber charter schools.
"There is a wide disparity in Pennsylvania," said Devora Davis, research manager of Stanford's Center for Research on Education Outcomes (CREDO), which conducted the study. "It's a much different distribution than we've seen nationally."
CREDO examined Pennsylvania's charter schools as a follow-up to a 2009 report on charter school performance in 16 states. The researchers have not evaluated New Jersey's charter schools, but Davis said they had been talking to education officials about obtaining access to state data.
The Pennsylvania analysis showed that 30 percent of charter students performed significantly better than regular public school students in reading and 25 percent in math. Those results are far above the national average of 17 percent for high-performing charter schools.
But, on average, the state's charter school students lag behind the gains of students in regular public schools - 39 percent of charter schools underperform their public school counterparts in reading and 46 percent in math.
Nationally, students at 37 percent of charter schools perform significantly worse in both.
Thirty percent of Pennsylvania charter students performed about the same as traditional public school students in reading and 28 percent in math.
Nationally, about half of charter students do no better or worse than peers in district-operated schools.