The average score for traditional public schools statewide was 77.1. Brick-and-mortar charter schools averaged 66.4 and cyber charters 46.8.
The profiles were released in October, but scores for more than 620 schools were suppressed after concerns were raised about accuracy.
This week, the state released all of the profiles.
Downingtown STEM scored 101.4.
"When I saw that every single kid passed the Keystone in algebra and literature and all but a couple passed biology, I knew we would be up there, but I didn't know we would be No. 1," said principal Art Campbell. "That's an amazing accomplishment. Our teachers and our kids work so hard."
Central High School in Philadelphia was just a fraction behind at 101.3. As expected, schools in wealthier suburban communities, or that filled desks mostly with high achievers, racked up the top scores.
Another STEM high school, in the Chester Upland School District, bottomed out at 15.8, while Chester Upland High School came in at 35.3 following a summertime public relations blitz touting improved academic standards in an effort to increase enrollment.
In a statement, Chester Upland superintendent Gregory Shannon noted that the results were of tests taken last year.
"This year we have created a new environment with a safe and orderly school culture that allows us to turn our full attention to academic achievement," he said. "It is our full expectation that we will see growth in our academic performance in this school year's round of assessment."
Of the 233 Philadelphia schools whose scores were released, a little more than 10 percent scored above 70, which acting state Education Secretary Carolyn Dumaresq has called a "mark of moving toward success."
Overall, nearly 73 percent of public schools statewide received a score of 70 or higher.
The gap in average scores among traditional schools, charters, and cyber charters shows that "charter schools, especially cyber charter schools, need to be held to the same accountability standards as traditional public schools so all students receive a quality education," said a release from the Pennsylvania School Boards Association.
Downingtown, whose schools serve 12,000 students from eight municipalities in Chester County, is better known as the town where parts of the cult horror movie The Blob were filmed than for academic conquests. Those usually fall to another Chester County district, Tredyffrin/Easttown, whose Conestoga High School is nationally recognized and whose profile was 95.9.
The 800-student Downingtown school accepts about half of those who apply. Applicants must have at least a C average, get a teacher recommendation, and write three essays.
The school requires that all of its 11th- and 12th-grade students enroll in the International Baccalaureate program, a rigorous course of study that is offered as an option at a handful of local schools, including Harriton in Lower Merion.
This year's seniors, who took the Keystone tests last year, make up the first graduating class.
The profile scores include results of the Pennsylvania System of School Assessment in grades 3-8, the new Keystone Exams in grade 11, and PASA, an alternate exam given to mentally or physically disabled children in grades 3-8 and 11.
The profile also takes into account other measures of student achievement, such as student academic growth from year to year, graduation rate, attendance rate, and promotion rate.
Campbell noted that being a magnet school was very different from being a large comprehensive high school with a variety of students, including special education and English Language Learners.
But he proudly pointed out that Downingtown's other two high schools, Downingtown East and Downingtown West, were in the top 9 percent of schools in the state.
"Which is also excellent," he said.
The Area's Top 10 Scoring Schools
1. Downingtown STEM Academy. Score: 101.4
2. Central High, Philadelphia School District. Score: 101.3
3. Merion Elementary, Lower Merion School District. Score: 100.6
4. Ithan Elementary, Radnor School District. Score: 100.2
5. Whitemarsh Elementary, Colonial School District.
6. Evergreen Elementary, Perkiomen Valley School District. Score: 99.3
7. Radnor Middle, Radnor School District. Score: 99.1
8. Lenape Middle, Central Bucks School District.
9. Central Bucks High East, Central Bucks School District. Score: 98.9
10. Strath Haven High, Wallingford-Swarthmore School District. Score: 98.6
To see the profile scores of schools throughout the region, go to www.inquirer.com/schoolprofiles