Geographic information systems (GIS) data/methods offer good promise for public health programs including obesity-related research. This study systematically examined their applications and identified gaps and limitations in current obesity-related research. A systematic search of PubMed for studies published before 20 May 2016, utilizing synonyms for GIS in combination with synonyms for obesity as search terms, identified 121 studies that met our inclusion criteria. We found primary applications of GIS data/methods in obesity-related research included (i) visualization of spatial distribution of obesity and obesity-related phenomena, and basic obesogenic environmental features, and (ii) construction of advanced obesogenic environmental indicators. We found high spatial heterogeneity in obesity prevalence/risk and obesogenic environmental factors. Also, study design and characteristics varied considerably across studies because of lack of established guidance and protocols in the field, which may also have contributed to the mixed findings about environmental impacts on obesity. Existing findings regarding built environment are more robust than those regarding food environment. Applications of GIS data/methods in obesity research are still limited, and related research faces many challenges. More and better GIS data and more friendly analysis methods are needed to expand future GIS applications in obesity-related research.