Because it was on a low-energy trajectory for its flyby of comet Wild 2 and return to Earth, and aided by a gravity-assisted boost maneuver as it flew by the Earth for the first time, the Stardust spacecraft needed only a relatively modest propulsion system. This was provided by ultra pure hydrazine (N2H4) monopropellant, a system often used in spacecraft, including the Space Shuttle.

The Stardust spacecraft is 3-axis stabilized in all mission phases, after separation from the launch vehicle. Stabilization is accomplished using eight 0.45 kgf thrusters and eight 0.1 kgf thrusters mounted in four clusters of 4 thrusters each. The primary attitude determination is accomplished using the star camera and the inertial measurement unit (IMU), with backed up from analogue sun sensors. The IMUs are only needed during trajectory correction maneuvers, and during the fly-through of the cometary coma when stars might be difficult to detect. Otherwise, the vehicle can be operated in an all-stellar mode.

The RAD6000 central processing 32-bit unit embedded in the spacecraft's Command and Data Handling (C&DH) subsystem provides computing capability for all spacecraft subsystems, including the payload elements. Electronic cards are provided to interface instruments and subsystems to the C&DH subsystem. 128 Mbytes of data storage are provided on the processor card, although the spacecraft uses approximately 20% of this for its own internal programs. The rest of the space in the memory is used for science programs and data storage for sending back to Earth 600 megabits (Mb) of images taken by the navigation camera, 100 Mb by the Comet Interstellar Dust Analyzer (CIDA) instrument and 16 Mb by the Dust Flux Monitor (DFM).

Primary communication between the Earth and the orbiter is through the Deep Space Network (DSN) X-band (up/down) link and the orbiter's deep space transponder developed for the Cassini spacecraft, a 15 Watt RF solid state amplifier, and a 0.6 meter (2 ft) diameter fixed high gain parabolic antenna.

Two non-gimbaled solar arrays were deployed immediately after launch. They provide 6.6 square meters of solar energy to power the Stardust spacecraft. One nickel-hydrogen (NiH2) 16 amp-hour battery using common pressure vessel (CPV) cell pairs provides power during eclipses and for peak power operations. The electrical power control electronics were derived primarily from the Small Spacecraft Technology Initiative (SSTI) spacecraft development.

The thermal control subsystem uses passive methods and louvers to control the temperature of the batteries and the solid state power amplifiers. Passive coatings as well as multi-layer insulation blankets are used to control other temperatures. Where needed, radiators are used to draw excess heat out of the spacecraft components to maintain a proper operating temperature.

The Stardust spacecraft structure is the shape of a rectangular box, with approximate dimensions of about 5 feet (1.7) meters long by a square cross-section of about 1 1/2 feet (0.66) meters on each side. Panels use graphite fibers with polycyanate as face sheets and aluminum honeycomb as the core.

Virtually all spacecraft subsystem components are redundant with critical items cross-strapped. The battery includes an extra pair of cells. A software fault protection system is used to protect the spacecraft from reasonable, credible faults. It also has resiliency built into it so many unanticipated faults could be accommodated for without disabling the spacecraft.