Background: Medication reconciliation is the process of comparing a patient's medication orders to all the medications that the patient has been taking. It is a patient-focused clinical care service rendered by healthcare practitioners to reduce medication-related patient harm and to improve patient outcomes. Assessment of community and hospital pharmacists' knowledge on medication reconciliation is needful to ascertain their knowledge of the concept and to serve as a template for intervention, if necessary. Methods: This study aimed at assessing medication reconciliation knowledge among community and hospital pharmacists. A cross-sectional study was carried out among pharmacists working at community and hospital pharmacies in a developing country, using a validated semi-structure questionnaire. Data was summarized using descriptive and inferential statistics (Chi square and independent-samples t-test) with the level of significance set at p < 0.05. Results: One hundred and thirty-three pharmacists participated in the study. Medication reconciliation knowledge assessment scores, out of a maximum obtainable score of 29, for the community and hospital pharmacists were 12.42 ± 4.99 and 14.9 ± 4.94 (p = 0.011), respectively. Only 18 (21.4%) community pharmacists and 13 (26.5%) knew the three steps involved in medication reconciliation. Thirty (35.7%) community pharmacists and 29 (59.2%) hospital pharmacists knew that medication reconciliation is a teamwork among all the healthcare practitioners, and not to be carried out by pharmacists or any of the other healthcare practitioners in isolation. Sixty-nine (82.1%) community pharmacists and 39 (79.6%) hospital pharmacists knew that dietary supplements must be considered in medication reconciliation. Majority, 55 (66.5%) of the community pharmacists and 22 (44.9%) hospital pharmacists had "poor" medication reconciliation knowledge. However, additional educational qualification, work experience and gender did not significantly influence pharmacists' knowledge of medication reconciliation. Conclusion: Knowledge of the pharmacists on medication reconciliation was poor. This could be a pointer to inadequate medication reconciliation practice among the study population. There is need to carry out an educational intervention among community and hospital pharmacists to address the medication reconciliation knowledge gaps identified.