Background <p>Despite the well-established benefits of initiating breastfeeding within the first hour of birth and of exclusive breastfeeding, many newborns across low- and middle-income countries do not receive timely or exclusive breastfeeding during the early neonatal period. Delayed initiation of breastfeeding and the introduction of prelacteal feeds remain common and are influenced by a range of maternal, neonatal, and health system factors. Exclusive breastfeeding for the first two days after birth (EBF-2d) has recently been introduced as a new infant feeding indicator; however, its prevalence and associated factors are not well understood in Nepal. This study aimed to examine the prevalence of, and factors associated with early initiation of breastfeeding and exclusive breastfeeding for the first two days after birth.</p> Methods <p>A community-based cross-sectional study was conducted using a structured questionnaire among 423 randomly selected mothers of children aged 6–23 months in a remote mountainous region of Nepal. Prevalence was reported using frequency distribution, and associations were examined using Chi-square tests followed by multiple logistic regressions.</p> Results <p>Children had lower odds of receiving EBF-2d if they were born low birthweight (Adjusted odds ratio (AOR): 0.33; 95% confidence interval (CI): 0.17, 0.63), born at home (AOR: 0.23; 95% CI: 0.08, 0.61), or their mothers had health issues hindering breastfeeding (AOR: 0.45; 95% CI: 0.23,0.90). Conversely, children had higher odds of receiving EBF-2d when mothers were assisted by a skilled health worker during birth (AOR: 3.23; 95% CI: 1.33, 7.82) and when mothers received antenatal counselling on exclusive breastfeeding (AOR: 2.18; 95% CI:1.16, 4.08). Similarly, children had lower odds of receiving EIBF if they had low birthweight (AOR: 0.36; 95% CI: 0.19, 0.68) but they had higher odds when childbirth was assisted by skilled health workers (AOR: 9.15; 95% CI: 3.84, 21.8), were born at health facility (AOR: 16.08; 95% CI: 5.80, 44.5), and when mothers received antenatal counselling on breastfeeding on demand (AOR: 2.55; 95% CI: 1.48, 4.41), antenatal counselling on exclusive breastfeeding (AOR: 2.33; 95% CI: 1.28, 4.23), and advice on avoiding artificial nipples (AOR: 4.49; 95% CI: 2.07, 9.75).</p> Conclusion <p>Breastfeeding practices in remote Karnali remain suboptimal, particularly among low birth weight infants and those born at home. Skilled birth attendance, institutional childbirth, and antenatal breastfeeding counselling were associated with improved early breastfeeding practices. Strengthening facility-based childbirth, ensuring skilled birth attendance, and enhancing antenatal counselling on optimal breastfeeding practices are essential for improving early breastfeeding outcomes.</p>