Medication errors are more likely to occur during patient’s transition of care. There was very little information about impact of medication reconciliation activities done for patients with chronic kidney disease (CKD) Stage IV-V during admission stage in Malaysian Primary Hospitals. The objective of this study is to evaluate the impact of clinical pharmacist’s medication reconciliation activities during hospital admission of patients with CKD stage IV-V. This cross-sectional study was carried out in two multidisciplinary wards (male & female ward) in Hospital Raub, Pahang over 12 months with ethical approval. A clinical pharmacist was assigned to enroll potential study subjects in both wards. Patients over 18 years old who had previous history of CKD Stage IV-V were included in the study after obtaining informed consent. Medication reconciliation was carried out by the clinical pharmacist within 24 working hours during the admission of study subjects. All detected medication discrepancies were further classified as “intended” or “unintended” after discussion with the prescribing medical officer. The Severity Level of each unintended medication discrepancy was rated by a visiting medical specialist. Twelve patients with CKD stage V were recruited to the study. A total of 49 medication discrepancies were identified and most (89.8%) were found to be unintended. The most common unintended medication discrepancy identified was omission error. Most of the unintended medication discrepancies (59.1%) was rated as “No potential harm”, while 40.9% were rated as “Potential for monitoring and/or Intervention to preclude harm”. None of the unintended medication discrepancy was rated as “Potential harm”. In conclusion, medication discrepancies were common during admission of patients with late-stage chronic kidney disease in a primary hospital. Medication reconciliation performed by clinical pharmacist during admission has a potential role in preventing potential harms that may arise from unintentional medication discrepancies.