Among the genetic and environmental risk factors, nutrition plays a crucial role in determining the timing of puberty. Early menarche onset (EMO) is defined as when girls reach menarche onset at an age which is earlier than the mean/median age of menarche, between 12 and 13 years of age, according to individual ethnicity. The present study examined the association between nutrient intake in childhood and EMO risk in healthy girls by performing a systematic review and meta-analysis of prospective studies. We screened EMBASE, Cochrane Library, PubMed/MEDLINE, and Web of Science databases for 16 eligible studies with all medium-to-high quality scores ranging from 3 to 5 of 6 possible points with 10,884 subjects. Higher intakes of energy (risk ratio (RR) = 3.32, 95% confidence interval (CI) = 1.74–6.34, I2 = 97%), and protein (RR = 3.15, 95% CI = 2.87–3.44, I2 = 0%) were associated with EMO risk. For each additional 1 g/day animal protein intake in childhood, the age at menarche was approximately two months earlier (β = −0.13, I2 = 55%), and high iron intake was associated with EMO (RR = 1.20, 95% CI = 1.03–1.40, I2 = 0%). Polyunsaturated fatty acid (PUFAs) intake was associated with EMO risk with a dose-response effect (RR = 1.25, 95% CI = 1.05–1.49, I2 = 44%). Girls with a high intake of fiber and monosaturated fatty acids (MUFAs) in childhood experienced later menarche onset (RR = 0.83, 95% CI = 0.69–1.00, I2 = 31%; RR = 0.66, 95% CI = 0.50–0.86, I2 = 0%, respectively). Thus, adherence to a high intake of animal proteins-, iron- and PUFA-rich food diet makes girls more likely to have EMO, while a high intake of fiber- and MUFA-rich foods may protect girls from EMO. Further studies are expected to investigate the role of specific types of PUFAs and MUFAs on EMO to promote healthy sexual maturity in girls.