Dosage Compensation (DC) in Drosophila melanogaster involves the precise transcriptional upregulation of the hemizygous X chromosome in males to levels that are two-fold via chromosome wide-targeting of the Male Specific Lethal (MSL) complex. An outstanding question in the field of Drosophila DC is how two-fold transcriptional upregulation across the male X chromosome is regulated. The nuclear pore protein (Nup) Megator (Mtor), has been linked to regulation of DC in Drosophila males, albeit debatably. The Nuclear Pore Complex (NPC) is a large protein complex embedded in the nuclear envelope, canonically known to regulate nucleocytoplasmic transport. A recent focus in the field has been on the intranuclear presence of Nups binding to and regulating expression of genomic targets. Mtor has been implicated in RNA biogenesis processes in yeast but whether Mtor affects gene expression in a DC specific manner in Drosophila remains unknown. Here, we set out to characterize Mtor’s gene regulatory role in the context of Drosophila DC. Using RNAi based depletion of Mtor in larval salivary glands, we have uncovered a male-specific role for Mtor as a negative regulator of dosage compensated, X chromosome gene expression. Upon Mtor depletion, we observed a unique chromosome wide, upregulation of X-linked genes in males via RNA-Seq. We observed a conserved biochemical interaction between MSL components and Mtor as well as genetic interactions between Mtor and MSL components where depletion of Mtor can partially rescue male lethality in MSL mutant backgrounds. By RNA FISH, we did not observe changes in mRNA export of X chromosome genes but did find transcription to be upregulated in Mtor depleted males 3-4 fold. This upregulation of expression was found to occur at the level of nascent transcription by nascent RNA sequencing. Our findings suggest that the mechanism by which this upregulation of expression occurs upon Mtor depletion is during the regulation of the first phosphorylation event of the RNA Polymerase II C-terminal domain, promoting transcription initiation. These findings demonstrate a physiological role for Mtor in the process of DC, as a transcriptional attenuator of X chromosome gene expression in Drosophila.