The Kepler mission will launch in 2007 and determine the distribution of earth-size planets (0.5 to 10 earth masses) in the habitable zones (HZs) of solar-like stars. The mission will monitor > 100,000 dwarf stars simultaneously for at least 4 years. Precision differential photometry will be used to detect the periodic signals of transiting planets. Kepler will also support asteroseismology by measuring the pressure-mode (p-mode) oscillations of selected stars. Key mission elements include a spacecraft bus and 0.95meter, wide-field, CCD-based photometer injected into an earth-trailing heliocentric orbit by a 3-stage Delta II launch vehicle as well as a distributed Ground Segment and Follow-up Observing Program. The project is currently preparing for Preliminary Design Review (October 2004) and is proceeding with detailed design and procurement of long-lead components. In order to meet the unprecedented photometric precision requirement and to ensure a statistically significant result, the Kepler mission involves technical challenges in the areas of photometric noise and systematic error reduction, stability, and false-positive rejection. Programmatic and logistical challenges include the collaborative design, modeling, integration, test, and operation of a geographically and functionally distributed project. A very rigorous systems engineering program has evolved to address these challenge. This paper provides an overview of the Kepler systems engineering program, including some examples of our processes and techniques in areas such as requirements synthesis, validation & verification, system robustness design, and end-to-end performance modeling.