The geomagnetic declination, inclination and total field data surveyed at the Croatian Geomagnetic Repeat Stations Network were reduced to 2008.5, 2009.5 and 2010.5 epochs by a well-known observatory-based and a proposed method, in instances when an influence of the differences of secular variations at a repeat station and at an observatory were not taken into account. The motivation came from distances and distribution of the nearby geomagnetic observatories. A technique for expanding vector systems on a sphere into basis functions, known as the Spherical Elementary Current System (SECS) method, was applied to obtain separation of the geomagnetic field variations into external and internal parts, over Croatia and surrounding countries. The aim of this work is to propose the SECS method for determination of the annual mean values of north, east and vertical components of Earth’s magnetic field at the Croatian repeat stations. The results of the SECS method were compared to an observatory-based method which assumes that the variations of components about their annual mean values at a repeat station are equal to those at a particular nearby reference observatory. For reducing a repeat station data by this simple method the Fürstenfeldbruck, Grocka and Tihany observatories were used, while for the SECS method additional three observatories were employed. The reduction methods were found comparable, while in the majority of instances the SECS method demonstrated smaller standard deviations of the components’ annual means. Besides, the annual mean values of the vertical component had the highest accuracies for both methods. The results indicate that the SECS method can be an acceptable method for data reduction to annual mean values.