Despite the dramatic reduction in Trypanosoma cruzi vectorial transmission in Brazil, acute cases of Chagas disease (CD) continue to be recorded. The identification of areas with greater vulnerability to the occurrence of vector-borne CD is essential to prevention, control, and surveillance activities. In the current study, data on the occurrence of domiciliated triatomines in Brazil (non-Amazonian regions) between 2007 and 2011 were analyzed. Municipalities' vulnerability was assessed based on socioeconomic, demographic, entomological, and environmental indicators using multi-criteria decision analysis (MCDA). Overall, 2275 municipalities were positive for at least one of the six triatomine species analyzed (Panstrongylus megistus, Triatoma infestans, T. brasiliensis, T. pseudomaculata, T. rubrovaria, and T. sordida). The municipalities that were most vulnerable to vector-borne CD were mainly in the northeast region and exhibited a higher occurrence of domiciliated triatomines, lower socioeconomic levels, and more extensive anthropized areas. Most of the 39 new vector-borne CD cases confirmed between 2001 and 2012 in non-Amazonian regions occurred within the more vulnerable municipalities. Thus, MCDA can help to identify the states and municipalities that are most vulnerable to the transmission of T. cruzi by domiciliated triatomines, which is critical for directing adequate surveillance, prevention, and control activities. The methodological approach and results presented here can be used to enhance CD surveillance in Brazil.