More than 115 million women across the world are borrowers of microfinance loans. However, there is concern that women from poor backgrounds who take loans may suffer from multiple challenges of physical and mental health burdens. In this qualitative study we aimed to identify the types of health challenges faced by active women borrowers of microfinance loans. Open ended questions were asked from 442 women across seven cities and four provinces of Pakistan. Categories were developed through the content analysis approach using NVIVO. We have been able to identify thirteen different health challenges faced by poor women borrowers under two broad headings of "environmental factors" and "healthcare delivery system." We recommend the introduction and expansion of different health and social development services by microfinance provider's to support the health needs of poor women clients. Women also need support from the Government of Pakistan in improving access to education, health coverage, and formal sector work opportunities. Our study implies increased health policy support for disadvantaged women borrowers of microfinance across the world.