The durability of brickworks, used as facing bricks, parapets, or chimneys, is a crucial aspect of the maintenance of buildings. Water absorption and penetration due to wind-driven rain, water rundown, and capillary rising can cause serious damages and a premature deterioration of porous clay bricks, and a significant increase in their thermal conductivity. Protective coatings for brickwork must provide enhanced hydrophobic properties without affecting moisture regulation and breathability of masonry. In the present work, a standardized type of facing clay brick was treated with two types of hydrophobic coatings based on a commercial perfluoropolyether oligomer containing alkoxysilane terminal groups, respectively, with or without an inorganic precursor, tetraethoxysilane, to generate in situ silica nanoparticles. The performance of the coating was assessed by multiple indicators, such as wetting delay, water absorption coefficient, protection degree by capillarity, contact angle, roughness and gloss, as a function of the amount of coating. Uncertainties analysis of indicators was carried out. Coating performance was assessed at different exposure times comparable to in situ real ones. Optimal amounts of coating were established to maximize the protection with the minimum quantity of polymer. As a result, a square meter of brick surface exposed to water for 2–4 h can absorb about 7–8 L of water. Very small amounts of PFPE coatings change the brick surface/water interactions, more than halving the absorbed water (0.5–2 l) and increasing the protection degree up to 80–100%. After longer exposure times, the reduction in absorbed water is basically higher when brick specimens are treated with organic/inorganic nanostructured hybrid PFPE coatings.