Eukaryotic elongation factor 1A (eEF1A) is an essential protein that facilitates translational elongation by delivering aminoacyl-tRNAs to ribosomes. Protein N-terminal methylation is an under-characterised post-translational modification, with only three, highly homologous, N-terminal methyltransferases known in eukaryotes.  Here we report a new eukaryotic protein N-terminal methyltransferase, Saccharomyces cerevisiae YLR285W, which methylates eEF1A at a previously undescribed high-stoichiometry N-terminal site and the adjacent lysine. Using parallel reaction monitoring (PRM) and MS/MS/MS (MS3), we unambiguously localised these modifications, showing that N-terminal trimethylation precedes dimethylation at the adjacent lysine. Deletion of YLR285W resulted in the loss of N-terminal and lysine methylation in vivo, whereas overexpression of YLR285W resulted in an increase of methylation at these sites. This was confirmed by in vitro methylation of eEF1A by recombinant YLR285W. Accordingly, we name YLR285W as elongation factor methyltransferase 7 (Efm7). This enzyme is a new type of eukaryotic N-terminal methyltransferase as, unlike the three other known eukaryotic N-terminal methyltransferases, its substrate does not have an N-terminal [A/P/S]-P-K motif. We show that the N-terminal methylation of eEF1A is also present in human; this conservation over a large evolutionary distance suggests it to be of functional importance. Indeed, proteomic analysis of the knockout of Efm7, with SILAC, reveals the role of this methylation in modulating the function of eEF1A.