Abstract Background. Although computed tomography (CT) has played a critical role in medical care since its introduction in the 1970s, its potential long-term risk of adverse health effects has been of concern. It is crucial to accurately estimate the radiation dose delivered to the patient’s critical organs to ensure the dose is As Low As Reasonably Achievable. However, organ-level dose calculation tools for pediatric and adult patients with various body sizes are rare. We extended the existing CT organ dose calculator, NCICT 1.0, which is based on reference-size phantoms, to include body size-specific pediatric and adult phantoms. Methods. We calculated body size-specific organ doses normalized to CTDI_vol by using a library of 158 pediatric and 193 adult computational human phantoms with various body sizes combined with a Monte Carlo radiation transport code, MCNP6. We also created a library of generic tube current modulation (TCM) profiles for the phantom library using a ray-tracing algorithm and implemented them into organ dose calculations. We validated organ doses for the body size-specific phantoms using those calculated from ten abdominal CT patients. We also evaluated potential dosimetric errors caused by only using reference phantoms for patients with different body sizes. Results. Organ dose coefficients and TCM profiles for 351 pediatric and adult body size-specific phantoms were implemented into NCICT 2.0. The dose coefficients from the ten abdominal CT patients agreed with those from the program within 13%. The organ doses for the overweight phantoms were overestimated by over 80% when only reference size phantoms were used. Conclusion. We confirmed that the upgraded dose calculator NCICT 2.0 could substantially reduce potential dosimetric errors caused by using only reference size phantoms. The program should be useful for the radiology community to accurately monitor organ doses for pediatric and adult CT patients with various body sizes.