Information about essential trace elements among children in many African countries, including the Democratic Republic of Congo (DRC), is limited. We aimed to measure the distribution and determinants of serum zinc (Zn), copper (Cu), and selenium (Se) concentrations in a representative sample of children under five years old. We conducted a community-based cross-sectional study in Popokabaka, DRC. Blood samples were drawn from 412 children. The serum concentrations of minerals were measured using inductively coupled plasma–mass spectrometry. The median concentrations (P25–P75) of Zn, Cu, and Se were 61.9 µg/dL (52.8–70.2), 145.5 (120.0–167.0) µg/dL and 5.3 (4.3–6.3) µg/dL. The CRP-adjusted prevalence of serum Se deficiency was 84.1% (95% confidence interval [CI] 81.4–87.0) and of Zn deficiency was 64.6% (95% CI 59.8–69.1%). Only a few children were Cu deficient [1.5% (0.6–3.2)]. Evidence of inflammation (C-reactive protein, >5 mg/L) was associated with a lower Se concentration and higher Cu concentration. Furthermore, serum Se concentration was positively associated with linear growth. The average Cu/Zn molar ratio (2:1) was twice that recommended. Children in western Popokabaka had higher Zn and Se levels than their eastern neighbors. Zinc and selenium deficiencies are common among children in Popokabaka and require attention and prioritization.