Ganymede is the only Solar System moon that generates a permanent magnetic field. Dynamics inside Ganymede’s magnetosphere is likely driven by energy-transfer interactions on its upstream magnetopause. Previously in Kaweeyanun et al. (2020), we created a steady-state analytical model of Ganymede’s magnetopause and predicted global-scale magnetic reconnection to occur frequently throughout the surface. Using the same model, this paper provides the first assessment of Kelvin-Helmholtz (K-H) instability growth on the magnetopause in isolation from reconnection effects. The linear K-H instability growth rate is calculated at Ganymede’s equatorial magnetopause flank points under the magnetohydrodynamic with finite Larmor radius effect (MHD-FLR) theory, which accounts for inter-flank growth rate asymmetry due to large gyroradii of Jovian plasma ions. The calculation gives growth rates between γ ≈ 0.01-48 /s with notable enhancement at the equatorial flank point closer to Jupiter. Then, the ideal MHD K-H instability onset condition is evaluated across the entire Ganymedean magnetopause. We find the conditions along both magnetopause flanks to be K-H favorable at all latitudes with growth rates similar to those at respective equatorial flank points. Using Mercury’s magnetopause case as a comparison, we determined that nonlinear K-H vortices are viable at Ganymede based on the calculated growth rates, but the vortex growth will likely be suppressed once global reconnection is taken into account.