Decoding how intelligence is engrained in the human brain construct is vital in the understanding of particular neurological disorders. While the majority of existing studies focus on characterizing intelligence in neurotypical (NT) brains, investigating how neural correlates of intelligence scores are altered by atypical neurodevelopmental disorders, such as Autism Spectrum Disorders (ASD), is almost absent. To help fill this gap, we use a connectome-based predictive model (CPM) to predict intelligence scores from functional connectome data, derived from resting-state functional magnetic resonance imaging (rsfMRI). The utilized model learns how to select the most significant positive and negative brain connections, independently, to predict the target intelligence scores in NT and ASD populations, respectively. In the first step, using leave-one-out cross-validation we train a linear regressor robust to outliers to identify functional brain connections that best predict the target intelligence score (p − value < 0.01). Next, for each training subject, positive (respectively negative) connections are summed to produce single-subject positive (respectively negative) summary values. These are then paired with the target training scores to train two linear regressors: (a) a positive model which maps each positive summary value to the subject score, and (b) a negative model which maps each negative summary value to the target score. In the testing stage, by selecting the same connections for the left-out testing subject, we compute their positive and negative summary values, which are then fed to the trained negative and positive models for predicting the target score. This framework was applied to NT and ASD populations independently to identify significant functional connections coding for full-scale and verbal intelligence quotients in the brain.