Allen Academy's Lower School academic program is an accelerated, integrated curriculum that focuses upon the foundation skills necessary for continuous academic growth and success. Language Arts, Reading, Social Studies, Mathematics, and Science are core subjects. Lower School students are also instructed in Music, Art, Spanish, Computer Education, and participate in Physical Education classes.

The lower elementary classrooms are self-contained, which provide for the nurturing element so greatly needed at this level. Upper Elementary students rotate to departmentalized classes and the course load prepares them for success at this level and future success in Middle School. Choir, student government, band and other extra-curricular offerings are provided at the upper elementary level as well as several clubs.