In this paper, we present three different compartmental models to model the pharmacokinetics of Indocyanine green (ICG) in cancerous tumors. We introduce a systematic and robust method to analyze ICG pharmacokinetics based on extended Kalman filtering (EKF) framework. We introduced information theoretic criteria for best compartmental model selection in terms of statistical fit. We tested our approach using the ICG concentration data acquired from four Fischer rats carrying adenocarcinoma tumor cells collected using near infrared (NIR) techniques. Our study indicates that, in addition to the pharmacokinetic rates and ICG concentrations in different compartments, EKF model may provide parameters that may be useful for cancerous tumor differentiation.