Superfluidity and superconductivity are genuine many-body manifestations of quantum coherence. For finite-size systems the associated pairing gap fluctuates as a function of size or shape. We combine the semiclassical periodic orbit theory and BCS theory in order to provide a parameter free theoretical description of pairing fluctuations in mesoscopic systems characterized by order/chaos dynamics. The theory accurately describes experimental observations of nuclear superfluidity (regular system), predicts universal fluctuations of superconductivity in small chaotic metallic grains, and provides a global analysis in ultracold Fermi gases.