The intelligent system for autonomous spacecraft operations includes an on-board Autonomous Operations subsystem integrated with an on-ground Web-based Remote Intelligent Monitor System (RIMS) providing interface between on-ground users and the autonomous operations intelligent system. The on-board Autonomous Operation subsystem includes an On-Orbit Checkout Engine (OOCE) unit and an Autonomous Tasking Engine (ATE) unit. Spacecraft Command Language (SCL) engine underlies the operations of the OOCE, ATE and RIMS, and serves as an executer of commands sequences. The OOCE uses the SCL engine to execute a series of SCL command scripts to perform a rapid on-orbit checkout of subsystems/components of the spacecraft in 1-3 days. The ATE is a planning and scheduling tool which receives requests for “activities” and uses the SCL scripts to verify the validity of the “activity” prior to execution, and scheduling the “activity” for execution or re-scheduling the same depending on verification results. Automated Mission Planning System (AMPS) supports the ATE operations. The ATE uses a priority schedule if multiple “activities” are to be executed.