Fertiliser use is an ambigious issue in agricultural economics with different arguments commonly given for and against it. The aim of this paper is to find the most important factors affecting fertiliser use in Lithuania, serving as a basis for our fertiliser tax modelling of Lithuanian family farms. Raw data from Lithuanian farms was collected from the Lithuanian Farm Accountancy Data Network (FADN) covering the years 2003–2017, and data from other selected countries was also found in the FADN database, although in this case, different years (2004–2016) were available. Results suggest the significant factors affecting fertiliser use on family farms in Lithuania differ significantly from other EU countries. Hence, our empirical results confirm that there is no unique methodology or unique set of financial instruments for fertiliser tax modelling among EU countries, and this should be taken into account in future studies. We also noticed that investment in land, the extent to which farm output consists of wheat, rye and field vegetables, the use of harvesters and finally, land quality should also be taken account in future fertiliser tax modelling.