Polyglutamine (polyQ) diseases, including Huntington's disease, are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster. RNAi-mediated silencing of TRMT2A ameliorated polyQ-induced toxicity and polyQ aggregation in flies. This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases. An in silico structure- and ligand-based lead discovery approach and computer-aided drug discovery (CADD) was used to identify TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined and Biacore experiments with the RRM were performed. The identified inhibitors were functionally validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Several candidate molecules were able to decrease cell death and ameliorate the aggregation of polyQ peptides in cultured cells comparable to the TRMT2A knockdown experiments. Among these, spermidine was identified as able to cause a decrease in the abundance of polyQ aggregates in SCA3-patient derived fibroblasts. Our work provides a first step towards a pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.