Pyrite is a common mineral with a higher density than most other minerals in the Eagle Ford Shale formation. Hence, if pyrite is not considered in the total organic carbon (TOC) estimation, based on density logs, it may lead to errors. In order to improve the accuracy of the TOC estimation, we propose an updated TOC estimation method that incorporates the concentration of pyrite and organic porosity. More than 15 m of Eagle Ford Shale samples were analyzed using Rock-Eval pyrolysis, X-ray fluorescence (XRF), and X-ray diffraction (XRD). TOC, elemental concentration, and mineralogical data were analyzed for a better understanding of the relationship between the concentration of TOC and pyrite content in the Eagle Ford formation. An updated petrophysical model—including parameters such as organic pores, solid organic matter, inorganic pores, pyrite, and inorganic rock matrix without pyrite—was built using the sample data from the Eagle Ford. The model was compared with Schmoker’s model and validated with the Eagle Ford field data. The results showed that the updated model had a lower root mean square error (RMSE) than Schmoker’s model. Therefore, it could be used in the future estimation of TOC in pyrite-rich formations.