Information about factors associated with condom use among Nepalese labor migrant couples that are considered being at high risk of HIV infection is not clearly understood. Therefore, we carried out a cross-sectional study to identify the factors associated with condom use among Nepalese labor migrant couples. A total of 266 wives of Nepalese labor migrants were invited for an interview. Hierarchical logistic regression analysis was performed to analyze data. We found that almost 39% of the women reported having used a condom while having sex with their husbands. Age was the only husband-related factor independently associated with condom use. School education, knowledge about HIV/AIDS, discussion of HIV with peers and sexual negotiation with the husband were the wife-related factors independently associated with condom use. Our findings highlight a clear need to develop effective HIV prevention interventions targeting illiterate labor migrant couples, with a particular emphasis on increasing women's ability to negotiate condom use.