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We study the action of S-duality on half-BPS Wilson loop operators in 5d$\mathcal{N}=1$ theories. The duality is the statement that different massivedeformations of a single 5d SCFT are described by different gauge theories, orequivalently that the SCFT points in parameter space of two gauge theoriescoincide. The pairs of dual theories that we study are realized by brane websin type IIB string theory that are S-dual to each other. We focus on $SU(2)$SQCD theories with $N_f \le 4$ flavors, which are self-dual, and on $SU(3)$SQCD theories, which are dual to $SU(2)^2$ quiver theories. From string theoryengineering we predict that Wilson loops are mapped to dual Wilson loops underS-duality. We confirm the predictions with exact computations of Wilson loopVEVs, which we extract from the 5d half-index in the presence of auxiliary loopoperators (also known as higher qq-characters) sourced by D3 branes placed inthe brane webs. A special role is played by Wilson loops in tensor products ofthe (anti)fundamental representation, which provide a natural basis to expressthe S-duality action. The exact computations also reveal the presence ofadditional multiplicative factors in the duality map, in the form of backgroundWilson loops.

Wilson loops in 5d $\mathcal{N}=1$ theories and S-duality