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Background This article reports on the use of the ‘neighborhood method’ to measure the prevalence and basic characteristics of children who became separated from their parents or usual caregivers subsequent to an attack by the M23 militia group in North Kivu, Democratic Republic of the Congo. Methods A two-stage household cluster survey was conducted in 522 households in North Kivu in August 2014. Heads of households were asked about separated children in their household, as well as the households of their two closest neighbors. Separation was tracked in terms of children who arrived into the households after the M23 attacks and children who departed from the households after the recall event without their parent(s) or usual caregiver. For a subset of 44 neighbor pairs, respondents were asked to report on the same household to assess inter-rater reliability. Data about primary respondents and their neighbors were assessed to determine whether the neighborhood method was a comparable, reliable and efficient alternative to a traditional household survey about separated children. Results The prevalence of separated children who arrived was 8.52 % [95 % CI: 6.75–10.75] in primary households and 4.46 % [95 % CI: 3.60–5.52] in neighbors’ households (p-value = 0.0000). The prevalence of separated children who departed was 4.98 % [95 % CI: 3.45–7.19] in primary households and 3.19 % [95 % CI: 2.27–4.48] in neighbors’ households (p-value = 0.0110). Kappa coefficients for the neighbor pairs indicated fair to moderate agreement for most demographic variables, but agreement was generally higher for variables related to current characteristics of the households than for variables describing the household in the past, especially before the M23 attack. Compared to a traditional household survey with similar power, the neighborhood method reduced data collection time by 50 % and lowered costs by 36 %. Conclusion This pilot showed that, for measuring separated children in North Kivu, the results from neighbor households significantly underestimated the prevalence of separation when compared to data collected from respondents directly. Reliability was mixed. Although the neighborhood method did not yield valid results in this setting, given the potential the method holds to save scarce resources in humanitarian settings, additional pilots to refine and evaluate its validity and reliability in settings with shorter recall periods are recommended.