Introduction Despite an overall decrease in the incidence of meningococcal disease within the European Union (EU) in recent years, it continues to be a public health concern due to the disease severity, outbreak potential, and peaks in incidence among infants and adolescents. Since pharyngeal carriage of meningococcal disease is the primary means of disease transmission, it is important to compare carriage data to disease data from the same region to inform future vaccination policy. We aim to characterize the recent state of meningococcal carriage within the EU by reviewing the prominent serogroups associated with pharyngeal carriage. Methods We conducted a systematic review of the literature and relevant conference abstracts to identify studies reporting on serogroup-specific meningococcal carriage among age groups and in high-risk settings (military, university, and Hajj) for 2007–2016. Additional data were requested from authors of meningococcal carriage studies in specific age groups to standardize age ranges. These data were then used to conduct age-specific meta-analyses to elucidate serogroup-specific carriage in various age groups. Independent random effects meta-analyses were conducted for key serogroups—A, B, C, W, X, and Y—using the Freeman–Tukey transformation and exact binominal confidence intervals. For studies not eligible for meta-analysis, a narrative synthesis was performed. Results In total, 15 studies of the 4965 identified met our inclusion criteria and reported carriage data among military personnel (N = 3), university students (N = 6), and/or defined age groups (N = 12) from EU countries. No study reported serogroup-specific carriage among Hajj/Umrah pilgrims. Overall carriage rates in military personnel were higher among new recruits in Greece (15.2%) than in professional soldiers in Poland (5.2–5.7%). Serogroups B (range: 1.6–6.8%) and Y (range: 0.5–1.4%) were the most prevalent serogroups in all military studies. Among university studies, overall carriage ranged from 10.4% in Greece in 2015 to 62% in England in 2009. Serogroups B, W, and Y were the most common key serogroups identified. Overall carriage rates in defined age groups were lowest among 10–12-year olds in England at approximately 3% and highest among studies from university-aged students (range: 13–62%). No studies were conducted among older adults. Data from eight studies were included in the meta-analyses. Four studies reported data among 11- to 17-year-olds (England N = 1, Italy N = 2, France N = 1), and seven among 18- to 24-year-olds (England N = 3, Italy N = 2, France N = 1, Portugal N = 1). In 11- to 17-year-olds, among key serogroups, serogroup B was most prevalent (1.92%, 95% CI: 1.26–2.71). The remaining key serogroups in this age group each had a prevalence of Conclusions The primary serogroups identified in the age groups responsible for transmission correspond to those with higher incidence within the EU: serogroups B and Y with W increasing in recent years. Surveillance of invasive disease and carriage studies should continue, especially in light of the introduction of new vaccines within many countries’ national immunization schedules. Since conjugate vaccines for serogroups A, C, W, and Y have been shown to induce herd immunity and decrease carriage for serogroups A and C, the national vaccine strategies targeting age groups at highest risk for carriage acquisition and transmission could further reduce the overall burden of disease. Additional studies are required to understand the impact of new meningococcal serogroup B vaccines on carriage and their breadth of protection against disease.