Background: The primary aim of Community Pharmacists’ participation in immunization is to contribute towards mitigating deaths associated with vaccine preventable diseases as well as expanding access to immunisation services. However, with the increasing Nigerian population, the global targets of reducing child mortality can significantly be achieved by periodically reviewing health systems performance to identify and address existing gaps. Objective: The general objective of the study is to identify the challenges encountered by Community Pharmacists in providing immunisation services in Calabar Metropolis of Cross River State. Method: A descriptive cross sectional study design was adopted for the study. Data were collected using a pre-tested semi-structured questionnaire from 68 community pharmacists which were selected using the purposive sampling technique. Data generated were synthesised and analysed using SPSS (version 20.0) and results were presented in frequency tables and charts. Fisher Exact test was used to test for association between variables at 0.05 alpha level. Results: Results showed that most community pharmacies have the resources to participate in immunization, only a few however had immunization administration record sheets 7(11.3%) and immunization record cards for patients 4 (6.5%). The finding also showed that lack of training 55 (88.7%); low awareness by the public of immunization services provided by the community pharmacist 44 (70.9%) and storage of vaccines 39 (62.9%) were the prominent perceived challenges to providing immunization in the community pharmacy. The association between lack of time (p =1.000, Fisher’s Exact test) and provision of immunization services was statistically not significant. Conclusion: Addressing identified challenges is pivotal to increasing and expanding accessibility and utilisation of immunisation services especially amongst the populace in resource limited settings.