Neurocysticercosis is a poorly understood infection of the central nervous system with Taenia solium larva, and the treatment often fails to kill all the parasitic larva. Most research on this infection has used patient-level data, looking at summaries of the encysted parasitic cysticercus burden. Cyst-level analysis is needed to identify factors that impact individual cyst trajectories and how that may vary based on characteristics of the patient, infection and cyst being followed. We disaggregated data on 221 cysts from 117 patients who participated in a trial evaluating the impact of albendazole treatment to identify factors that impact cyst evolution over time from the active to the degenerating and calcified phases, and eventual resolution. We found that having calcified cysts at baseline was associated with a faster rate of transition from the degenerative phase to calcified phase or resolution. Age and sex were not associated with cyst evolution in the main effect analysis, but after stratifying on treatment we found that the direction of some associations by patient age and sex was reversed for patients in the albendazole arm compared to those in the placebo arm. These findings suggest that differences in host immune response by sex and age as well as by past exposure, potentially indicated by having calcified cysts together with active cysts at baseline, are important to cyst evolution and may be modified by treatment. Future research is needed to assess if these differences suggest distinct treatment recommendations.