Background: The World Health Organization recommends initiation of breastfeeding within 1 hour of birth and exclusive breastfeeding up to 6 months of age. Infant feeding practices, including suboptimal breastfeeding practices, are associated with stunting. Rate of stunting was highest in the Mid-western region and lowest in the Eastern region of Nepal. This study aimed to assess the breastfeeding practices in these two regions, as well as to identify factors associated with partial breastfeeding. Methods: We conducted a health facility-based cross-sectional study in the Mid-western and Eastern regions of Nepal from December 2017 to May 2018. Investigators administered a pre-tested questionnaire among consecutive 574 mother-infant dyads at different levels of health facilities. We dichotomized the breastfeeding pattern to partial breastfeeding and full (exclusive or predominant) breastfeeding. We conducted multivariable logistic regression to identify factors associated with partial breastfeeding within 6 months of age. Results: There were 574 infants included in the study, all of which received at least some breastfeeding. Only 23.2% of infants were exclusively breastfed until 6 months, with 28.2% predominantly breastfed and 48.6% partially breastfed. Partial breastfeeding rate was 52.3% in the Mid-western region and 44.4% in the Eastern region. Breastfeeding was initiated within an hour from birth in 67.2% of infants. One-quarter of infants were given pre-lacteal feed, honey being the commonest. Knowledge of the recommended duration of exclusive breastfeeding was inadequate in 16, and 65% of mothers reported breastfeeding problems in the first 6 months. Firstborn and low birth weight infants had a significantly higher rate of partial breastfeeding. Partial breastfeeding was also higher when infants were not breastfed within 1 hour from birth, mothers reported having breastfeeding-related problems or had inadequate knowledge of the duration of exclusive breastfeeding. Conclusion: Nearly half of the infants were fully breastfed at 6 months of age in Nepal. The rate of partial breastfeeding was higher with inadequate knowledge on duration of exclusive breastfeeding or late initiation of breastfeeding or perceived breastfeeding problems. Hence, programs should address knowledge and practice gaps in breastfeeding practices, particularly among mothers of low birth weight and firstborn infants.