In-line with the World Health Organization’s (WHO) Global Technical Strategy for Malaria (2016–2030), Vietnam is striving to eliminate malaria by 2030. Targeting appropriate interventions in high-risk populations such as forest and forest-fringe communities is a critical component of malaria elimination efforts in Vietnam. In 2016, a household-level malaria indicator survey was conducted in Phu Yen Province, Vietnam with the aim of assessing the knowledge, behaviors and associated risks of malaria infection among priority mobile and migrant populations (MMPs) working and sleeping in forests and on farms. A total of 4211 people were included in the survey, comprised of 1074 heads of households and 3137 associated household members. Of the 1074 head-of-household respondents, 472 slept in a forest, 92 slept on a farm, 132 slept in both forests and farms, and 378 slept at their villages within the last 12 months. Age, literacy, and occupation were significantly different among those who slept in a forest versus on a farm. Of 301 respondents who answered questions about malaria risk factors at sleeping sites, 35% were somewhat aware of malaria prevention practices, but only 4% could recall at least four malaria prevention messages. Among the same group of 301 respondents, only 29% used nets and only 11% used treated nets. Ownership and use of nets among forest-goers was significantly lower than those who slept on a farm or in their village. Huts without walls were significantly prominent forest sleeping site locations (POR = 10.3; 95% CI 4.67–22.7). All respondents who slept in a forest requested standby malaria drugs and one-third of them self-treated without blood testing. Results from this study highlight the importance of capturing relevant location-specific data among priority populations such as remote forest and farm going mobile and migrant populations in Vietnam. Data regarding behavioral practices, knowledge, preventative measures, and intervention coverage at remote-area transmission sites must be routinely captured to effectively monitor progress and refine targeted intervention strategies accordingly.