Breakfast skipping is a commonly reported dietary habit among adolescents despite this life stage marked by critical growth and development. Limited comparable evidence exists from low- and middle-income countries (LMICs), where the detrimental effect of inadequate diets remains a major public health challenge. We conducted a systematic review to assess the scientific evidence available from LMICs regarding the association of breakfast skipping and consumption habits and anthropometry- and nutrition-related outcomes in adolescents 10–19 years old. Electronic searches for relevant studies were conducted on MEDLINE, EMBASE, CINAHL, CENTRAL and Web of Science from the date of database inception until June 28, 2023. Additionally, reference lists of included studies and gray literature were searched. We included studies of all designs that compared breakfast skipping and consumption habits among adolescents aged 10–19 years in LMICs. Exclusion criteria included the following: review articles, if the target population age was outside the WHO definition of adolescents, assessed only lunch or dinner consumption, skipped any other meal besides breakfast, only collected point prevalence data, did not include a breakfast consumer control group, or co-interventions were inconsistent across breakfast habit groups. The primary outcomes were body mass index (BMI in kg/m2), also defined categorically as underweight, normal weight, overweight and obese or as BMI-for-age (z-score) and anemia (defined according to Hemoglobin (Hb) levels in different age groups for boys and girls). Secondary outcomes included other adiposity measures and nutrient concentrations or deficiencies. Title screening, data extraction, and risk of bias assessment were conducted in duplicate. The risk of bias was evaluated using the NHLBI Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. Random-effects meta-analysis models were used to pool data for each outcome measure from the included studies. Standardized mean differences with 95% confidence intervals (95% CI) were calculated for continuous outcomes, while odds ratios (OR) with 95% CIs were computed for dichotomous outcomes. The certainty of the evidence for each outcome was appraised using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Our search yielded 3604 records, and 41 studies met our inclusion criteria. Among these, 39 cross-sectional studies and two prospective cohort studies were eligible, with 36 providing data for meta-analysis. Overall, there was very low certainty of evidence regarding the association between breakfast consumption habits and the risk of being overweight/obese, mainly due to the risk of bias and inconsistency. Adolescents who infrequently ate breakfast (0–2 days/week) were twice as likely to be overweight/obese (OR: 2.05, 95% CI: 1.61–2.61; I2 = 85%; n = 15 studies) compared to regular breakfast consumers (5–7 days/week), while irregular breakfast consumers (3–4 days/week) had 32% higher likelihood of being overweight/obese (OR: 1.32, 95% CI: 1.16–1.50; I2 = 59%; n = 9 studies). The odds of non-daily breakfast consumers being overweight/obese were 38% higher than daily breakfast consumers (OR: 1.38, 95% CI: 1.19–1.59; I2 = 54%; n = 10 studies). The odds of developing anemia were significantly higher for adolescents irregularly consuming breakfast compared to regular breakfast consumers (OR: 2.85, 95% CI: 1.71, 4.76; I2 = 0%), with very low certainty of the evidence from two studies, limited by a very small sample size. Few studies reported on the association of breakfast skipping with other secondary adiposity outcomes (e.g., waist circumferences, waist-to-height ratio). We found very low certainty of evidence that breakfast skipping increases the risk of overweight/obesity and anemia, primarily derived from cross-sectional studies. There is a paucity of evidence regarding breakfast habits and nutritional outcomes among adolescents in LMICs. Further cohort or intervention studies are warranted to elucidate the relationship between breakfast skipping and the risk of overweight/obesity, as well as other anthropometric and adiposity measurements within this demographic. Emphasis should also be placed on evaluating nutritional outcomes as a part of these assessments to better inform public health policy and programming best practices for adolescents to ensure the health and well-being of the next generation. Breakfast integrated within school feeding programs may be well positioned as a double-duty solution to tackle malnutrition in all its forms among adolescents.