The common approach to model occupants behaviors in buildings is deterministic and consists of assumptions based on predefined fixed schedules or rules. In contrast with the deterministic models, stochastic and agent based (AB) models are the most powerful and suitable methods for modeling complex systems as the human behavior. In this paper, a co-simulation architecture is proposed with the aim of modeling the occupant behavior in buildings by a stochastic-AB approach and implementing an intelligent Building Energy Management System (BEMS). In particular, optimized control logics are designed for smart passive cooling by controlling natural ventilation and solar shading systems to guarantee the thermal comfort conditions and maintain energy performance. Moreover, the effects of occupant actions on indoor thermal comfort are also taken into account. This study shows how the integration of automation systems and passive techniques increases the potentialities of passive cooling in buildings, integrating or replacing the conventional efficiency strategies.