The main task of this paper is to examine housing affordability and housing policy application in neglected border cities in Jordan. After the Iraq war in 2003 and the Syrian civil war in 2011, many border cities accommodated a large number of refugees in their urban context over different periods of time. The lack of affordable housing and the increase in unemployment was the main challenges for its vulnerable communities. Border cities are facing different development challenges but applying the same housing policy as metropolises. The paper studies the economic attributes and social characteristics of Mafraq city to analyze housing obstacles. It concludes that houses are unaffordable in these border cities and housing policies need modifications. The paper recommended that housing affordability in border cities must include community participation and sufficient financial aid to low-income families. In order to maintain houses affordable in border cities, the real estate market, community participation, urban planning, and promotion of tourism are all essential.