In recent years, several outbreaks of hepatitis C virus (HCV) infections have been observed among HIV-infected men who have sex with men (MSM) in Europe. In the Netherlands, high incidence rates of 10/1,000 person-years are reported. In this analysis, we describe whether acute HCV is linked to specific transmission networks. A total of 50 Dutch HIV-infected MSM, diagnosed with acute HCV genotype 1a between 2013 and 2014, were included. Target enrichment for viral nucleic acid separation and deep sequencing were used to recover whole HCV genomes. Phylogenetic trees were constructed by use of the maximum likelihood method. Pairwise distance matrices were generated by use of the Kimura-2 parameter distance estimation method. The consistency of the phylogenetic clustering was tested by bootstrap analysis with 1,000 replicates. A cluster was defined as having a genetic distance of at most 1.5 per cent and bootstrap values of 100 per cent. The most recent common ancestor was estimated with a coalescent-based model with a Bayesian statistical framework. Four transmission clusters were identified that included a total of 38 patients (76% of the total). The clusters were indicative of recent outbreaks, as highlighted by small genetic distances and a most recent common ancestor after the year 2000, when the first cases of HCV infection in HIV-infected MSM were reported. The HCV epidemic among HIV-infected MSM is a young epidemic, with most of the acute infections linked within the four major transmission networks. Prevention strategies identifying and targeting these transmission networks can potentially curb the epidemic.