Most empirical equations used for wave runup predictions have been developed from measurements at straight sandy beaches in unlimited fetch environments. While there are empirical equations to predict wave runup on gravel beaches, they have not been tested for prediction of wave runup on pocket gravel beaches, in limited-fetch environment, which can be found around Mediterranean. This paper addresses this lack of measurements on this type of beaches and examines the alongshore variability of wave runup. Wave runup measurements were made using video observations along 3 cross-sectional profiles on the pocket beach of Ploče, Croatia. The measurements have shown that the wave runup can vary for about 71% even around the centerline of the pocket beach. This variability is due to beach orientation and alignment of beach profiles to the prevailing wave direction, as well as difference in beach slope. Comparison of wave runup predictions from five well-known empirical equations and field measurements showed significant underprediction (up to NBIAS = −0.33) for energetic wave events, and overall high scatter (up to NRMSE = 0.38). The best performing wave runup equation was used for further refinement outside the original parameter space by including the Goda wave peakedness parameter (Qp). The newly developed empirical equation for wave runup reduced the NBIAS to 0 and the NRMSE by 31% compared to the original equation (developed equation metrics: R = 0.91, NBIAS = 0, NRMSE = 0.2, HH = 0.2 on the study site). This empirical equation can potentially be used for design of coastal structures and artificial beaches in similar environments, but further measurements are needed to test its applicability to a range of forcing and environmental conditions.