Home cage condition influences the central nervous system of experimental animals. However, little is known about the effect of home cage size and bedding material on fear-related behaviors. Thus, in this study, the effects of home cage size (large or small) and/or bedding material (paper or wood) on acquisition, retrieval, extinction, and spontaneous recovery of contextual fear memory were investigated in both male and female mice. The present study demonstrated that males housed in small cages with wood bedding showed a low fear response during fear extinction when compared to males housed in small or large cages with paper bedding. In females, mice housed in small cages with wood bedding showed low fear response during fear conditioning and extinction when compared to mice housed in large cages with paper bedding. Moreover, small cages with wood bedding, but not small or large cages with paper bedding, prevented the spontaneous recovery of fear memory in females. Thus, home cage conditions, and particularly bedding material, influence contextual fear extinction and spontaneous recovery. This finding may help to obtain reproducibility of results by researchers and explain discrepancies of results among research groups.