  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 massive
deformations of a single 5d SCFT are described by different gauge theories, or
equivalently that the SCFT points in parameter space of two gauge theories
coincide. The pairs of dual theories that we study are realized by brane webs
in 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 theory
engineering we predict that Wilson loops are mapped to dual Wilson loops under
S-duality. We confirm the predictions with exact computations of Wilson loop
VEVs, which we extract from the 5d half-index in the presence of auxiliary loop
operators (also known as higher qq-characters) sourced by D3 branes placed in
the brane webs. A special role is played by Wilson loops in tensor products of
the (anti)fundamental representation, which provide a natural basis to express
the S-duality action. The exact computations also reveal the presence of
additional multiplicative factors in the duality map, in the form of background
Wilson loops.
