This study introduces a twin enrichment strategy based on dual-template molecularly imprinted polymer-assisted solid-phase microextraction coupled with dispersive liquid-liquid microextraction (MISPE-DLLME) for the simultaneous extraction and determination of favipiravir and remdesivir in biological matrices (blood and urine), followed by high-performance liquid chromatography with ultraviolet detection (HPLC-UV) analysis. The dual-template molecularly imprinted polymer (DT-MIP) was synthesized via precipitation polymerization and comprehensively characterized using Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), field-emission scanning electron microscopy (FESEM), Brunauer-Emmett-Teller (BET) surface area analysis, simultaneous thermal analysis (STA), and X-ray diffraction (XRD). Under optimized conditions, including pH 2.00 ± 0.1, 10.0 mg of MIP, 200 ± 5 μL of 1-dodecanol, 500 ± 10 μL of methanol, and an extraction time of 10.0 ± 0.5 min, the method afforded high recoveries of 103-110% with relative standard deviations (RSDs) below 5% (n = 3). The method showed excellent sensitivity, with limits of detection of 1.0 ng/mL for favipiravir and 0.40 ng/mL for remdesivir and limits of quantification of 3.3 ng/mL and 1.3 ng/mL, respectively. Selectivity was evaluated against ten structurally related drugs (ibuprofen, gemfibrozil, paracetamol, diazepam, clobazam, methocarbamol, theophylline, naproxen, dimenhydrinate, and cinnarizine) at various concentration ratios, and the DT-MIP displayed superior recognition performance compared with the corresponding non-imprinted polymer (NIP). Analysis of clinical samples yielded acceptable recoveries and precision, confirming the reliability of the proposed method and its potential applicability in therapeutic drug monitoring of COVID-19 antivirals.