Understanding the neurobiology of opioid use disorder (OUD) using resting-state functional magnetic resonance imaging (rs-fMRI) may help inform treatment strategies to improve patient outcomes. Recent literature suggests time-frequency characteristics of rs-fMRI blood oxygenation level-dependent (BOLD) signals may offer complementary information to traditional analysis techniques. However, existing studies of OUD analyze BOLD signals using measures computed across all time points. This study, for the first time in the literature, employs data-driven machine learning (ML) for time-frequency analysis of local neural activity within key functional networks to differentiate OUD subjects from healthy controls (HC). We obtain time-frequency features based on rs-fMRI BOLD signals from the default mode network (DMN), salience network (SN), and executive control network (ECN) for 31 OUD and 45 HC subjects. Then, we perform 5-fold cross-validation classification (OUD vs. HC) experiments to study the discriminative power of functional network features while taking into consideration significant demographic features. The DMN and SN show the most discriminative power, significantly (p < 0.05) outperforming chance baselines with mean F1 scores of 0.7097 and 0.7018, respectively, and mean AUCs of 0.8378 and 0.8755, respectively. Follow-up Boruta ML analysis of selected time-frequency (wavelet) features reveals significant (p < 0.05) detail coefficients for all three functional networks, underscoring the need for ML and time-frequency analysis of rs-fMRI BOLD signals in the study of OUD.