Objectives: This study aimed to examine the association between maternal health behaviors and neonatal outcomes among the Indonesian population. Methods: Articles were collected from PubMed, EBSCO, ProQuest, DOAJ, and GARUDA. Funnel plots and Egger’s tests analyzed indications of publication bias. A Mantel–Haenszel random-effects model was used to see the overall effect size of exposures on outcomes. Heterogeneity was seen based on I2. Data collected from articles included the author, year of publication, location of the study, study design, number of samples, risk factors, and effect sizes. Results: We identified 24 relevant studies, including eight from the primary databases and 16 from an additional database. A total of 12 studies were included in the meta-analysis, examining the association between maternal health behaviors and neonatal outcomes. The pooled odds ratio (OR) for passive smoking and low-birth-weight (LBW) was 3.41 (95% CI: 1.75–6.63, I2 = 40%, four studies). The pooled OR for incomplete antenatal care (ANC) and LBW was 6.29 (95% CI: 2.11–18.82, I2 = 70%, four studies). The pooled OR for incomplete ANC and neonatal mortality was 2.59 (95% CI: 1.01–6.66, I2 = 93%, four studies). Conclusions: The results indicated that pregnant women with incomplete ANC had a higher risk of LBW and neonatal mortality, and those who were passively exposed to smoking had a higher risk of LBW. Further investigations are needed, considering the high heterogeneity found, and additional meta-analyses should be based on the variations of socio-demographic conditions.