The high catalytic activity of cobalt-doped MoS2 (Co–MoS2) observed in several chemical reactions such as hydrogen evolution and hydrodesulfurization, among others, is mainly attributed to the formation of the CoMoS phase, in which Co occupies the edge-sites of MoS2. Unfortunately, its production represents a challenge due to limited cobalt incorporation and considerable segregation into sulfides and sulfates. We, therefore, developed a fast and efficient solid-state microwave irradiation synthesis process suitable for producing thin Co–MoS2 flakes (∼3–8 layers) attached on nitrogen-doped reduced graphene oxide. The CoMoS phase is predominant in samples with up to 15 at% of cobalt, and only a slight segregation into cobalt sulfides/sulfates is noticed at larger Co content. The Co–MoS2 flakes exhibit a large number of defects resulting in wavy sheets with significant variations in interlayer distance. The catalytic performance was investigated by evaluating the activity towards the hydrogen evolution reaction (HER), and a gradual improvement with increased amount of Co was observed, reaching a maximum at 15 at% with an overpotential of 197 mV at −10 mA cm−2, and a Tafel slope of 61 mV dec−1. The Co doping had little effect on the HER mechanism, but a reduced onset potential and charge transfer resistance contributed to the improved activity. Our results demonstrate the feasibility of using a rapid microwave irradiation process to produce highly doped Co–MoS2 with predominant CoMoS phase, excellent HER activity, and operational stability.