Seaweeds have been explored as a natural resource of compounds of interest due to their bioactivities. Although many studies report the interest and the application of seaweeds in various areas, from food or human health to the economy, these data mostly focus on raw extracts and not on specific compounds, such as seaweed pigments. Fungal infections of the skin, nails, and hair caused by dermatophytes are the most common fungal infections worldwide. These pathologies require long periods of topical and/or systemic treatment associated with adverse effects and increased antifungal resistance. So, this study had two objectives: the first was to isolate and characterize the pigments of the seaweeds Calliblepharis jubata and Fucus vesiculosus; the second was to assess their antifungal activity. The extraction of pigments was performed using a method of extraction by exhaustion, and the purification was achieved via column chromatography. Three techniques were used to characterize the pigments: thin-layer chromatography (TLC), UV–visible spectrophotometry, and Fourier-transform infrared spectroscopy (FTIR). The antifungal activity against the three most common dermatophytes, Trichophyton rubrum, Trichophyton mentagrophytes, and Microsporum canis, was evaluated using a microdilution methodology, following the EUCAST international standards. It was possible to observe that the extracts obtained from the seaweed C. jubata, corresponding to the purified pigment phycobiliprotein, and the crude extract (an enriched extract) showed antifungal activity against the three fungal agents of human skin infection.