Early initiation of combination antiretroviral therapy (ART) with long-term viral suppression may lead to seronegativity in grown-up children with perinatally acquired HIV (PHIV). This study aimed to determine the frequency and associated factors of seronegativity in Thai children, adolescents and young adults with PHIV. A cross-sectional HIV serological study was performed in children, adolescents and young adults two years or older who were receiving ART with undetectable HIV-RNA for at least one year from August 2018 to August 2019. Medical records were extracted for multivariate analysis of independent factors for seronegativity. Of 110 patients, 50 male, median (range) age was 18.4 (4.8 to 26.6) years, 8 (7.3%) were seronegative, and 1 (0.9 %) was inconclusive. The seronegative group had a younger median (range) age at ART initiation: 3.0 (1.0 to 12.0) versus 40.0 (2.0 to 207.0) months, p = 0.045; and shorter median (range) duration from ART initiation to viral suppression: 16.8 (7.2 to 42.0) versus 55.2 (6.0 to 214.8) months, p = 0.036. Multivariate analysis identified younger age at ART initiation (aOR 0.69, 95% CI 0.49 to 0.98, p = 0.038) and shorter time to viral suppression after ART initiation (aOR 0.94, 95% CI 0.89 to 0.99, p = 0.019) as independent factors associated with HIV seronegativity. Of the infants who initiated ART < 3 and between three and six months of age, 50% and 26.7% became seronegative respectively. HIV seronegativity was observed in children and adolescents with PHIV who initiated ART early in infancy and had rapid and sustained virological response. Awareness of this phenomenon will help avoid inappropriate treatment interruption on the basis of negative antibody testing.