Background Device-based therapies have been used for onychomycosis patients with intolerance to systemic treatments. Photodynamic therapy (PDT) improves onychomycosis, while fractional carbon dioxide (FrCO2) augments the topical drug delivery. Comparative studies between PDT alone and laser-assisted one are lacking. Objective We aimed to evaluate the efficacy of PDT alone versus FrCO2-assisted PDT for treatment of onychomycosis. Methods Twenty-one patients with bilateral onychomycosis of toenails with nearly the same degree of affection were enrolled in this prospective intra-patient-controlled study. The right affected toenail was treated via PDT alone. The left toenail was treated via a FrCO2 followed immediately by PDT. The sessions were bimonthly for a total of six sessions. Direct microscopy, fungal cultures, clinical evaluation, onychomycosis severity index scoring, and patient’s satisfaction were assessed before and 12 weeks after the last session. Results Both treatments reduced significantly the onychomycosis severity index (p < .05) without significant difference between them. The improvement in nail appearance and patient’s satisfaction were higher in laser-assisted PDT than PDT alone (p < .05). Conclusion Both treatments effectively reduced the severity of onychomycosis with a high degree of safety and tolerability. Fractional CO2-assisted PDT enhanced the clinical outcome via improving the nail appearance and patient’s satisfaction. Key message Photodynamic therapy has a good success rate in clearing onychomycosis. Addition of fractional CO2 to photodynamic therapy improves the nail appearance and induces better satisfaction to treatment.