Knowing the actual level of mental workload is important to ensure the efficacy of brain-computer interface (BCI) based cognitive training. Extracting signals from limited area of a brain region might not reveal the actual information. In this study, a functional near-infrared spectroscopy (fNIRS) device equipped with multi-channel and multi-distance measurement capability was employed for the development of an analytical framework to assess mental workload in the prefrontal cortex (PFC). In addition to the conventional features, e.g. hemodynamic slope, we introduced a new feature - deep contribution ratio which is the proportion of cerebral hemodynamics to the fNIRS signals. Multiple sets of features were examined by a simple logical operator to suppress the false detection rate in identifying the activated channels. Using the number of activated channels as input to a linear support vector machine (SVM), the performance of the proposed analytical framework was assessed in classifying three levels of mental workload. The best set of features involves the combination of hemodynamic slope and deep contribution ratio, where the identified number of activated channels returned an average accuracy of 80.6 in predicting mental workload, compared to a single conventional feature (accuracy: 59.8). This suggests the feasibility of the proposed analytical framework with multiple features as a means towards a more accurate assessment of mental workload in fNIRS-based BCI applications. © 2001-2011 IEEE.