This study was addressed to evaluate the temporal and spatial changes in regional cerebral blood flow (rCBF) of patients with neuropsychiatric systemic lupus erythematosus (NPSLE). Our objective was to correlate the subtracted SPECT coregistered to MRI features (SISCOM) with demographic, clinical and laboratory findings to shed light upon the pathophysiological evolution of the NPSLE. Twenty-six NPSLE patients with MRI and pre and post-treatment brain SPECT with [99mTc]Tc-ECD. SISCOM features were categorized as improvement,worsening, activation and/or deactivation of rCBF findings. Patients mean age of 43.19 years and 65.38% white were evaluated. The patients mean age at onset of SLE was 26.05 and 42.29 for NPSLE. The mean time between the onset of SLE and first NPSLE symptoms was 5.57 years. The disease has already been initiated as NPSLE in 4 patients. The SLEDAI average score was 31.69 and the SLICC/ACR-DI score was 6.96. The patients underwent an average of 9.23 cyclophosphamide. The SISCOM findings showed functional and pathological states on different brain regions. The rCBF changes were not associated with index scores. There was, however, a trend towards an association between lower SLEDAI scores with improvement and higher SLEDAI with worsening in SISCOM. Also, a trend of association between lower SLICC score with improvement, and higher SLICC with worsening. The female gender was predictive of activation and worsening, separately, and deactivation and worsening in a set. Non-white patients were predictive of worsening. The seizure was predictive of deactivation separately, and deactivation and worsening in a set. Finally, normal C3 was a predictor of improvement. The present study showed dynamic brain changes in NPSLE patients. SISCOM technique showed improved rCBF in some brain areas, and worsening, activation and deactivation in anothers. There were associations between rCBF changes and gender, skin colour and complement C3, and association trends with SLEDAI and SLICC scores.