This study was undertaken to assess the effect of artemether treatment on plasma lipid profile in malaria infection. While the importance of lipid to plasmodial infective processes and metabolism is being increasingly appreciated, little is known about the attendant effect of chemotherapy on plasma lipid profile. Thirty patients with uncomplicated malaria were chosen from two secondary health-care facilities in Yobe State, Nigeria with informed consents and ethical clearance. Based on predetermined inclusion criteria patients were given 3.2 mg/kg of artemether with 1.6 mg/kg on subsequent days for a total of five days. This was done after the collection of urine and blood samples for urinalysis, malaria parasite density count and serum lipid analysis. A follow-up was planned seven (7) days from first dose during when clinical assessment and repeat malaria parasite density count and serum lipid analysis were done. Data were analyzed with statistical package for social scientist and Microsoft Excel spread sheet while level of significance at p ≤ 0.05 was calculated using paired t-test. Serum HDL cholesterol concentration recorded a significant decline of 0.13 mmol/L from a pre-treatment mean concentration of 1.17 mmol/L (p < 0.04). Triglyceride, total cholesterol, LDL-cholesterol, VLDL-cholesterol showed increment or reductions that were not significant. The clinical cure rate was 50% and mean percentage reduction in parasitaemia was 52%. A possible explanation for this low cure rate could be resistance, unfavorable pharmacokinetic disposition or lack of full adherence. A trial with complete parasite clearance, possibly using artemisinin-based combinational therapy would provide a more compelling result.