Fucoidanase is a promising biocatalyst for several biotechnological applications. Crude fucoidanase production by Dendryphiella arenaria was optimized using a natural low-cost medium composed of Cystoseira trinodis and natural seawater. The results showed that seaweed biomass concentration and incubation period were the most significant factors affecting fucoidanase production. At the optimized conditions [seaweed biomass (4.25% w/v), seawater concentration (100% v/v), and incubation period (2 days)], the fucoidanase production was 3.43 U/mL. The crude fucoidanase exhibited a wide pH (3–9) stability with residual activity > 58%. The enzyme showed a good thermostability at 40 and 50 °C with half-lives of 239.02 and 115.52 min, respectively. Several parameters of thermal inactivation kinetics and thermodynamics were calculated, and suggested that the enzyme would be thermostable. Additionally, enzymatic extract containing fucoidanase was used for the enzymatic saccharification of the brown algal biomass in terms of seaweed particle size, solid/liquid ratio, and enzyme dosage. The maximum reducing sugars obtained was 57.11 mg/g. To the best of our knowledge, this is the first report regarding fungal fucoidanase optimization mediated saccharification of a brown seaweed.