MacroH2A has been linked to transcriptional silencing, cell identity, and is a hallmark of the inactive X chromosome (Xi). However, it remains unclear whether macroH2A plays a role in DNA replication. Using knockdown/knockout cells for each macroH2A isoform, we show that macroH2A-containing nucleosomes slow down replication fork progression in the Xi reflecting the higher nucleosome stability. Moreover, macroH2A1, but not macroH2A2, promotes synchrony of origin firing in the Xi, and macroH2A1 downregulation increases DNA loop sizes corresponding to replicons. This relates to macroH2A1 regulating replicative helicase loading during G1 by interacting with it. We mapped this interaction to a phenylalanine in macroH2A1 that is not conserved in macroH2A2 and the C-terminus of Mcm3 helicase subunit. We propose that macroH2A1 association with origins enhances the licensing of pre-replication complexes via DNA helicase loading onto the Xi and/or macroH2A1 counteracts unloading of the helicase by maintaining the chromatin silenced state.