This systematic review and meta-analysis summarises the literature on parental acceptance, parental hesitancy, uptake, and the associated factors of seasonal influenza vaccination (SIV) among children aged 6–59 months. Studies were sourced from the following platforms: PubMed, Web of Science, MEDLINE, and EMBASE databases. A random-effects model was used to evaluate the prevalence and 95% confidence intervals (CI) of parental acceptance, parental hesitancy, and SIV uptake in the last flu season and lifetime among children. A total of 36 studies were included for analysis. The overall prevalence was 64% for parental acceptance (95% CI: 51–75%), 34% for parental hesitancy (95% CI: 22–48%), 41% for SIV uptake in the last flu season (95% CI: 33–50%), and 46% for SIV uptake in a lifetime (95% CI: 20–74%). Associated factors of parental acceptance/hesitancy and uptake included the age of the children or parents, parental education level, household income level, ethnicity, and other modifiable factors, including perceived benefits, perceived barriers, perceived severity, perceived susceptibility, and cues to action related to SIV. Meta-regression analyses revealed regional differences in parental acceptance (Americas: 79% vs. Asia: 60%). The results provided implications informing us of the development of intervention programs targeting parents to improve SIV coverage among young children.