Parental vaccine hesitancy (VH) remains a barrier to full population inoculation, hence herd immunity against the SARS-CoV-2 virus. We aimed to determine parental VH rate, subgroups and influencing factors related to the BNT162b2 COVID-19 vaccine among their young adolescents (12–15 years old) in Qatar. A retrospective, cross-sectional study was conducted from 17 May to 3 June using vaccination booking records of 4023 young adolescents. Sociodemographic characteristics (i.e., age, sex, and nationality), health status and BNT162b2 COVID-19 vaccination booking status were analysed. Among respondents, the VH rate was 17.9%. Parents of 12-years adolescents were more hesitant (21.6%) as compared to the 13- (16.0%) and 15- (15.2%) years groups (p < 0.05). Parents of adolescents belonging to Gulf Countries (97% Qatari) were more hesitant (35.2%) as compared to the four remaining groups of nationalities (Asiatic; excluding Gulf Countries), North-African, African (excluding North-African), and European/American/Oceanian, 13.3–20.4%, (p < 0.001). Parental VH rates were higher when adolescents suffered from chronic disease as compared to those without the chronic disease (21.3% vs. 17.4%, p < 0.05) or who previously were COVID-19 infected as compared to non-previously COVID-19 infected (24.1 vs. 17.5%, p < 0.01). Results of logistic regression revealed that age groups, nationalities, and recovery from COVID-19 were the main predictors of VH level. Precisely, parents of 12 years old adolescents were 38% more likely to be hesitant as compared to the parents of the 15 years old adolescents (OR = 1.38; 95%CI: 1.12–1.70). Compared with the Gulf countries, parents of adolescents belonging to the other nationality categories; namely North-African, African, Asiatic and European/American/Oceanian were 48% (95%CI: 0.36–0.65), 41% (95% CI: 0.27–0.62), 38% (95%CI: 0.29–0.50) and 34% (95% CI 0.21–0.56) less likely to be hesitant, respectively. Furthermore, parents of young adolescents being previously COVID-19 infected were 37% more likely to be hesitant as compared to those with no previous COVID-19 infection (OR = 1.37; 95%CI: 1.02–1.84). Effective communication strategies specifically targeting Gulf Country populations, parents of younger children aged 12 years and of those with chronic disease or have been previously infected with COVID-19 are crucial to build community trust and vaccine confidence, thereby increasing COVID-19 vaccine uptake.