Recently, there has been significant progress made in regard to chemical protocols for the detection and investigation of epitranscriptomic modifications, such as new breakthroughs in high-throughput sequencing methods, base-specific chemistries, and spectroscopy. Herein, we describe the development in methodology for probing epitranscriptomic modifications. We characterize the prevalent RNA modifications and the most important breakthroughs in epitranscriptomics. Further, a summary of the available approaches for detection is presented, with a strong focus on the newest methodology for each modification. We characterize analytical methods for the following modifications: N6-methyladenosine (m6A), 1-methyladenosine (m1A), 5-methylcytidine (m5C), 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C), 5-carboxycytidine (ca5C), inosine (I), pseudouridine (Ψ), and 2′-O-methylation (Nm). These are framed in the context of mRNA and other coding and non-coding RNAs. These epitranscriptomic modifications often determine the structure, life span, and function of RNAs, which are major regulatory molecules of cellular biology.