In order to examine the behavior of reinforced concrete (RC) elements and structures, a significant variety of finite element analysis tools have been developed. The majority of these material models are significantly reliant on a set of empirical factors, the presence of which is critical for describing material behavior. Typically, these parameters are associated with post-peak concrete properties such as strain softening, tension stiffening, shear-retention capacity, etc. In the current investigation, a non-linear finite element analysis is utilized in order to estimate the flexural response of the RC beam. In order to perform this, two frequently employed software packages ABAQUS and ATENA 3D are utilized. To facilitate the direct comparison, three numbers of beams were considered for simulation in order to analyze the response against monotonous loading. Each beam specimen was 2100 mm long, 125 mm wide and 250 mm deep. The levels of replacement for natural aggregates were set at 0%, 50%, and 100%. The substitution for natural aggregates was confined to coarse fractions of aggregates only. The beam specimens were subjected to four-point loading and the zone of constant moment was determined to be 600 mm, which is equivalent to the one-third of their effective span. Moreover, to investigate the possibility of improving the simulation, the literature-described constitutive relationship for recycled aggregate concrete and the measured constitutive relationship for reinforcing steel were used as an inputs. The present investigation goal is to examine the generality, application, and capacity of the FE models currently in use to produce accurate predictions of the behavior of structural concrete.