As part of the 2030 Agenda, higher education has been conceptualised as one of the ways to overcome the social disparities experienced in rural areas in Colombia. Thus, in concordance with the benefits of this level of education, the state has been designing public policies during the last few years, in order to facilitate access to undergraduate programmes to these populations, focusing mainly on the implementation of the virtual modality. In this context, it is recognised that access itself is not enough, but that continuance and timely graduation are required to materialise the benefits obtained along with a higher education degree; hence, dropout is a subject of interest for study, especially due to the high rates existing in the rural student population. Therefore, the event of dropout becomes an obstacle to social change and transformation in rural areas. Thus, this article aimed to identify which individual, institutional, academic and socio-economic characteristics influence rural student dropout in virtual undergraduate programmes in Colombia. For this purpose, an exploratory, quantitative and cross-sectional study was proposed, with a sample of 291 students to whom a student characterisation instrument and a classroom evaluation instrument were applied. With these data, it was proceeded to establish which of them had deserted, constituting the extraction of the sample of the study, which were 168. With the information, an exploratory factor analysis, hierarchical cluster analysis and descriptive statistics were used to establish which explanatory variables are involved in the dropout of this type of student. The results showed that the academic variables analysed do not have an impact on the event, while marital status (associated with family obligations), age, social stratum, work obligations, parents’ level of education and type of work, income and type of employment relationship of the student, and, finally, the number of people who depend on the family’s income do.