Objective To compare the strain and gender differences between the ICR and C57BL/6J mice in the chronic fatigue syndrome model, and provide experimental evidence for the selection of model animals for chronic fatigue syndrome. Methods Mice were injected intraperitoneally with polyinosinic-polycytidylic acid (poly I:C) every three days and swam daily. The modeling was performed for 15 consecutive days, during which the weight and food intake of the mice were measured, and fatigue scores were assessed. After the modeling was completed, behavioral tests were carried out, including exhaustive swimming, tail suspension, mechanical pain threshold, and elevated plus maze. Results Compared with the control group, the exhaustion time of both strains of model mice in exhaustive swimming significantly decreased, the immobility time in tail suspension significantly increased, the mechanical pain threshold significantly decreased, the open arm entry time and frequency of the elevated plus maze in model male mice significantly decreased. The weight of model male C57BL/6J mice significantly decreased. The weight of model female ICR mice increased after the significant reduction. The exhaustion time of control C57BL/6J mice was significantly lower than that of control ICR mice. The immobility time of model C57BL/6J mice was significantly higher than that of model ICR mice. Conclusion There are differences between the two strains of mice in weight, fatigue level, and depression. Among the same strain of mice, there are differences between males and females, and the anxiety level of males is higher than that of females.