Recent studies have implicated distinct RNA-related mechanisms in several pathologies, opening new avenues for therapeutic intervention. Emerging data highlights the importance of epitranscriptomic mechanisms such as RNA methylation along with the discovery of coding and non-coding RNA transcripts that modulate numerous cellular processes. Current drug discovery assays for many RNA-related targets rely on cumbersome labels such as antibodies, fluorescent reporters, or radioisotopes that drive up costs and generate high rates of false positive data. Here, we describe a label-free and ultra high-throughput assay that combines self-assembled monolayers (SAMs) with matrix assisted laser desorption ionization (MALDI) mass spectrometry—a technique termed SAMDI—that offers unique and quantitative solutions for RNA drug discovery. We first showcase the development of a robust SAMDI assay to measure RNA methyltransferase activities. Next, we highlight how SAMDI delineates distinct RNA nuclease mechanisms. Finally, we describe an affinity selection mass spectrometry (ASMS) approach using SAMDI to reveal non-covalent small molecule binders to distinct RNA transcripts. Each approach is amenable to an ultra high-throughput readout capable of screening millions of compounds. Taken together, SAMDI is an enabling technology to drive RNA drug discovery towards the clinic.