The well-established Trypanosoma brucei (T.b.) brucei GVR35 mouse model of human African trypanosomiasis was used throughout this study. Briefly, 45 female CD-1 mice were infected by intraperitoneal injection of 2 × 104 parasites in 100 μL phosphate buffered saline glucose (PBS-G). The animals were divided into three cohorts and assigned to study; the neuroinflammatory reaction (n = 20), the trypanosome load (n = 20) or BBB function (n = 5). Each cohort was further divided into sub-groups (n = 5) to investigate disease progression at 7, 14, 21 and 28 days post-infection. Only one group was allocated to MRI as serial scans were performed on individual animals at each time point. Uninfected animals were included with the neuroinflammation (n = 4) and MRI (n = 3) studies to act as normal controls.