Natomas Charter School is currently comprised of five very diverse and unique programs. Each program acts as a "school within a school," deploying its own type of innovative instructional delivery system.
- Star Academy (Star): Site-based, TK-5 (adding grades 4 and 5 for the 2014-2015 school year)
- Pursuing Academic Choices Together (PACT) Academy: Nonsite-based, Grades K-8
- Leading Edge Middle School Academy (LE): Site-based, Grades 6-8
- Performing and Fine Arts Academy (PFAA): Site-based, Grades 6-12
- Virtual Learning Academy (VLA): Nonsite-based, Grades 9-12