RNA polymerase II (RNAP II) pausing is essential to precisely control gene expression and is critical for development of metazoans. Here, we show that the mA RNA modification regulates promoter-proximal RNAP II pausing in Drosophila cells. The mA methyltransferase complex (MTC) and the nuclear reader Ythdc1 are recruited to gene promoters. Depleting the mA MTC leads to a decrease in RNAP II pause release and in Ser2P occupancy on the gene body and affects nascent RNA transcription. Tethering Mettl3 to a heterologous gene promoter is sufficient to increase RNAP II pause release, an effect that relies on its mA catalytic domain. Collectively, our data reveal an important link between RNAP II pausing and the mA RNA modification, thus adding another layer to mA-mediated gene regulation.