We have used the Weather Research and Forecasting (WRF) model to simulate the climate of the Kerguelen Islands (49° S, 69° E) and investigate its inter-annual variability. Here, we have dynamically downscaled 30 years of the Climate Forecast System Reanalysis (CFSR) over these islands at 3-km horizontal resolution. The model output is found to agree well with the station and radiosonde data at the Port-aux-Français station, the only location in the islands for which observational data is available. An analysis of the seasonal mean WRF data showed a general increase in precipitation and decrease in temperature with elevation. The largest seasonal rainfall amounts occur at the highest elevations of the Cook Ice Cap in winter where the summer mean temperature is around 0 °C. Five modes of variability are considered: conventional and Modoki El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), Subtropical IOD (SIOD) and Southern Annular Mode (SAM). It is concluded that a key mechanism by which these modes impact the local climate is through interaction with the diurnal cycle in particular in the summer season when it has a larger magnitude. One of the most affected regions is the area just to the east of the Cook Ice Cap extending into the lower elevations between the Gallieni and Courbet Peninsulas. The WRF simulation shows that despite the small annual variability, the atmospheric flow in the Kerguelen Islands is rather complex which may also be the case for the other islands located in the Southern Hemisphere at similar latitudes.