Despite their pivotal roles in gene regulation, the precise timing of mRNA modifications during biogenesis has remained elusive due to the lack of methods that can simultaneously resolve modification status and RNA processing states at the single-molecule level. Here we describe two complementary nanopore-based approaches to establish a temporal framework for mRNA modification. First, we developed SWARM (Single-molecule Workflow for Analysing RNA Modifications) (Prodic et al. 2026), an AI-based tool that overcomes the high false-positive rates plaguing modification detection. By employing a training strategy that accounts for signal crosstalk from non-target modifications and incorporates orthogonally validated cellular signals, SWARM enables high-precision detection of m6A and pseudouridine (Ψ) at single-nucleotide and single-molecule resolution and outperforms existing tools on rigorous cellular benchmarks. Second, to place these modifications in time, we created dFORCE (direct Fractionated Observation of RNA Coupled to Elongation) (Sethi et al. 2025), a technique that separates transcriptionally engaged pre-mRNA from mature, polyadenylated transcripts, allowing us to pinpoint the order of processing events on a transcriptome-wide scale. Applying these technologies across cell lines, mammalian tissues, and targeted perturbation experiments with splicing and modification enzyme inhibitors reveals two key temporal principles of RNA modification. First, we find that m6A deposition substantially precedes splicing catalysis, with m6A accumulating near-cytoplasmic levels on unspliced pre-mRNA. Crucially, the canonical suppression of m6A near exon boundaries is already in place before splicing and the deposition of the exon junction complex, challenging prevailing models of how m6A topology is established. Second, we discover a splicing-shaped mode of Ψ deposition in which TRUB1-mediated pseudouridylation near exon boundaries preferentially occurs after exon-exon ligation, driven by local RNA structure stabilisation in spliced transcripts. We validate this mechanism using both nascent RNA sequencing and in vitro biochemical assays. Together, these findings suggest that m6A and Ψ modifications follow distinct temporal trajectories during mRNA maturation, arguing against a globally coordinated epitranscriptomic code and instead pointing to a more intricate, stepwise regulatory logic. and challenge models of widespread coordination between these marks. By integrating high-precision detection with temporal resolution, our integrated approach provides a robust framework for decoding the dynamic life of RNA.