A simple, highly efficient and tunable microwave-assisted conversion of seaweed-derived agarose into 5-hydroxymethyl furfural (5-HMF) or levulinic acid (LA), depending on the reaction conditions, is reported. The proposed system could be fine-tuned for the selective production of 5-HMF (ca. 51% yield) in the absence of any catalyst or alternatively to levulinic acid (64% yield) with the simple addition of 1% v/v sulfuric acid, both under optimized aqueous microwave irradiation conditions (10 min, 180 °C). Additionally, galactose could also be generated as the main product (45–77%) depending on the temperature and the addition of catalytic amounts of sulfuric acid. A plausible reaction mechanism is provided in which the formation of intermediates from the hydrolysis of agarose is critical to obtain 5-HMF and LA as final products.