The present study was undertaken to assess the current supply chain system of pharmaceuticals and vaccines in Pakistan in terms of structure, process, and outcomes, as well as related barriers and solutions for an effective supply chain system. A qualitative study was designed to explore stakeholders’ perceptions selected using the snowball sampling technique. A semi-structured interview guide was used to interview these respondents at a convenient time and place. After data collection, recorded interviews were transcribed verbatim and subjected to thematic analysis. The results highlighted that the standard operating procedures (SOPs), checklists, and government guidelines were available at different levels, except for community pharmacies. Timely delivery of quality products and services along with market reputation, experience, and authorization were the key criteria used for supplier selection and evaluation. Good inventory management, financial models, effective coordination, training, and skill development programs were identified as key factors responsible for an efficient supply chain process. Availability of vaccines, their appropriate temperature monitoring, and transportation are also highly compromised in Pakistan. The results of the present study concluded that the current supply chain system in Pakistan is not up to the mark; major factors include poor forecasting and inventory control, delayed order placement, lack of training, inadequate involvement of professionally qualified staff, inadequate financing and procurement processes, and poor coordination and integration among all stakeholders.