Cracks develop in concrete piles under lateral static loading as the tensile stress exceeds the concrete strength, causing a decrease in the pile’s flexural rigidity and influencing the load–deflection behavior. This paper presents a three-dimensional finite-element analysis (FEA) performed by PLAXIS 3D (version 2021) to investigate the impact of concrete cracking on the load–deflection behavior of laterally loaded piles in rock mass. Two FEA models were established to assess the influence of concrete cracking on load–deflection behavior. In the first model, nonlinear rock mass behavior was coupled with linear pile behavior (FEANL), while in the second model, nonlinear rock mass behavior was coupled with nonlinear pile behavior (FEANN). The three-dimensional (3D) FEA models were verified with a full-scale test case study for a deep-water pile foundation. The FEANN yields a more accurate simulation of measured deflection than the FEANL. A single run of The FEANN typically requires an entire day of computational time. Thus, a simplified approach was proposed to minimize the computational time process by incorporating the relationship of the change in pile flexural rigidity versus the bending moment (EI–M) into FEANL. In addition, the available EI–M relationships in the literature, such as the American Concrete Institute (ACI) method and beam theory, were evaluated by the EI–M relationship derived from the FEANN. The beam theory yields a lower estimate of pile flexural rigidity than the ACI method. The predicted deflection obtained through the simplified approach exhibits good agreement with the measured deflection utilizing the EI–M relationship derived from the FEANN. On the other hand, the EI–M relationship obtained from the beam theory overestimates the deflection compared to those obtained from the EI–M relationships of the ACI method and FEANN.