To achieve post-disaster recovery of rural households in developing countries, it is necessary to understand the recovery conditions and the factors that play significant roles in the decision-making process. The aim of this paper is (1) to explain the transition of the residential status (i.e., type of places or houses in which affected households stay) after the disaster event and (2) to reveal the factors affecting the housing decisions. 124 rural households in Nepal affected by the 2015 Gorkha earthquake were interviewed to understand the residential status transition up to two and a half years after the earthquake. As a result, more than 50 transition patterns were observed. Social relations in the community were important immediately after the earthquake, followed by the physical resources and subjective factors. Financial resources became influential at a later stage of recovery. The number of households that repaired or rebuilt their houses boosted one year after the earthquake. However, the households who moved to unrepaired houses did not upgrade to repaired or rebuilt houses. This implies that the disparity in residential status among affected households had been determined even before they left the temporary houses and began the recovery process. The results suggest that, for the prevention of recovery disparity, it is essential to support the recovery of individual households before the community starts the process, identifying their priorities and urgent needs and considering their circumstantial conditions. Thus, this study provides empirical data for effective recovery of vulnerable rural communities after disasters.