Objective This study was conducted to determine the relationship between their serum zinc levels and the CD4% in a cohort children living with HIV. Methods One hundred asymptomatic, anti-retroviral Therapy (ART) naïve children living with HIV (participants) aged 5–60 months who were enrolled into the Paediatric HIV clinic of The University of Nigeria Teaching Hospital were recruited in the study over a 10-month period. Blood samples were collected in the morning from non-fasting participants and serum zinc levels were analysed using Atomic Absorption Spectrophotometer. The CD4% was ascertained using the CD4% easy count kit on the Partec® Cyflow Counter machine. Data were analysed using Statistical Package for the Social Sciences version 19. Result The median (IQR) serum zinc level for the participants was 55.5 µg/dl (49.75) while their median (IQR) CD4% was 27.79% (18.67). Males had a median (IQR) CD4% of 24.29% (19.10) which was significantly lower than those of females [32% (20.59) (p = 0.047)]. No significant relationship was found between CD4% and zinc levels among the subjects (r = −0.061, p = 0.557). Conclusion Serum zinc levels of asymptomatic ART naïve children living with HIV have no relationship with their CD4%.