A data acquisition and analysis protocol for quality control (QC) of functional magnetic resonance imaging studies is presented. Two sets of data are acquired, single-timepoint data for measurement of signal-to-ghost and signal-to-noise ratios, and multiple-timepoint data for measurement of short-term drift. Since manual data analysis can be time consuming and an impediment to regular QC, an automated data processing scheme is presented. The use of automated Shewhart charting is proposed to identify significant changes in each parameter over the long term. The protocol has successfully identified system faults and deteriorations undetected by conventional QC.