Background: Since 2009, the incidence of meningococcal serogroup W disease has increased rapidly in the UK because of a single strain (the so-called original UK strain) belonging to the hypervirulent sequence type-11 clonal complex (cc11), with a variant outbreak strain (the so-called 2013 strain) emerging in 2013. Subsequently, the Netherlands has had an increase in the incidence of meningococcal serogroup W disease. We assessed the temporal and phylogenetic associations between the serogroup W outbreaks in the Netherlands and England, and the historical serogroup C outbreaks in both countries. Methods: For this observational cohort study, we used national surveillance data for meningococcal serogroup W and serogroup C disease in the Netherlands and England for the epidemiological years (July to June) 1992–93 to 2015–16. We also did whole genome sequencing and core genome multilocus sequence typing (1546 loci) on serogroup W disease isolates from both countries for surveillance years 2008–09 to 2015–16. We used Poisson regression to compare the annual relative increase in the incidence of serogroup W and serogroup C between both countries. Findings: In the Netherlands, the incidence of meningococcal serogroup W disease increased substantially in 2015–16 compared with 2014–15, with an incidence rate ratio of 5·2 (95% CI 2·0–13·5) and 11% case fatality. In England, the incidence increased substantially in 2012–13 compared with 2011–12, with an incidence rate ratio of 1·8 (1·2–2·8). The relative increase in the Netherlands from 2014–15 to 2015–16 was 418% (95% CI 99–1248), which was significantly higher than the annual relative increase of 79% (61–99) per year in England from 2011–12 to 2014–15 (p=0·03). Cases due to meningococcal serogroup W cc11 (MenW:cc11) emerged in 2012–13 in the Netherlands. Of 29 MenW:cc11 cases found up to 2015–16, 26 (90%) were caused by the 2013 strain. For both the current serogroup W outbreak and the historical serogroup C outbreak, the increase in incidence started several years later ...