St. Thomas has 240 students from prekindergarten to eighth grade but has space for 450. Fifty-seven percent of the students tested at grade level in math, while 49 percent are at grade level in reading.
St. Helene-Incarnation enrolls 480 students but could accommodate 600. Forty-two percent of its students tested at grade level in math, and 52 percent did so in reading.
The average in the same tests for the city's Catholic elementary schools is 64 percent in math and 59 percent in reading.
Both schools are part of a network of 14 Catholic schools in impoverished neighborhoods the nonprofit Independence Mission Schools began operating for the Archdiocese of Philadelphia last summer.
The partnership also is giving $68,000 to Center City's Independence Charter School, one of the city's top charters, to lay the groundwork to expand. The charter is not related to Independence Mission Schools.
The K-8 charter with 814 students will use the money to plan and explore asking the School Reform Commission for permission to open another K-8 school or a high school.
Philadelphia School Partnership executive director Mark Gleason said in a statement: "These grants address the unique needs and opportunities of two school models in both the public and private sector and the demand from families for more high-quality schools."
Founded in 2010, the partnership set a goal of raising $100 million to ensure more city students have access to high-quality schools. Its Great Schools Fund aims to add 35,000 seats in successful public, private, and charter schools by 2016-17.
Funding comes from a variety of sources, including the Bill and Melinda Gates Foundation, the Walton Family Foundation, and the William Penn Foundation.