Microbial desalination cell (MDC) is an environmentally friendly technology and a new method for desalination. The aim of this research is to investigate the extent of removal of arsenic (As) from aqueous solutions by MDC. To examine the efficiency of the process, synthetic As were prepared with concentrations of 100–600 μg/L in deionized water. The removal efficiency was examined at retention times of 30–120 min, at psychrophilic, mesophilic, and thermophilic temperatures and dissolved oxygen of 2–6 mg/L. The real water sample of Bardsir region in Kerman as well as the synthetic wastewater sample was experimented with to examine removal efficiency under the optimal conditions. The optimal conditions for removal of As were obtained as 600 mg/L of As, 6 mg/L of dissolved oxygen, temperature of 25–30 °C, and retention time of 120 min. Under these conditions, As removal efficiency in the synthetic samples of As, real water sample of Bardsir region, and synthetic wastewater sample was obtained as 75, 68, and 56%, respectively. Considering the relatively high efficiency of MDC in removal of As and its advantages including being environmentally friendly and saving energy, it is an effective method in removal of As from aqueous solutions.