The treatment of human African sleeping sickness is complicated by a post‐treatment meningo‐encephalitis that may be fatal. Using a mouse model this study assesses the use of the non‐steroidal anti‐inflammatory drug, azathioprine, in the management of this post‐treatment reaction. Female NIH mice treated with the trypanocidal compound diminazene aceturate (40 mg/kg), 28 days after infection, developed a similar post‐treatment reaction to that seen in humans. Administration of azathioprine (100 mg/kg) for 5 days before and 5 days after trypanocidal chemotherapy abrogated the pathology in the central nervous system although this returned approximately 15 days after cessation of azathioprine. Activated astrocytes associated with the later stages of the infection did not appear to be affected by the use of azathioprine.