Ancient churches represent an important part of the cultural and architectural heritage of a territory. Therefore, it is necessary to recover and preserve them to transmit their historical values to future generations. The performance evaluation in seismic prone areas and the interventions design are aimed at reducing churches vulnerability and ensuring their usability. In this paper, two different numerical methods, proposed by the current Italian Directive containing the Guidelines for assessment and reduction of cultural heritage seismic risk, are applied on a case study, an existing brick masonry church having in plan a basilica configuration and located in Southern Italy. In particular, linear kinematic analysis is applied, focusing on two potential failure mechanisms. The investigations performed, aimed at evaluating masonry churches seismic performance, highlight that the assumptions made influence the activation multiplier of macro-element response mechanism, in fact it may significantly vary, and that also a minimization process of the activation multiplier is needed.