Background: Pneumococcal vaccination rates in the United States (US) remain suboptimal, especially for adults aged 19 to 64 with high-risk medical conditions. Community-pharmacy-based immunization services increase vaccine access, particularly in rural areas. This study describes the provision of pneumococcal immunization services, assesses the processes used to identify and confirm patient eligibility, and determines barriers to immunization services in rural community pharmacies. Methods: A cross-sectional survey was emailed to members of the Rural Research Alliance of Community Pharmacies, located in the southeastern US. The survey assessed which pneumococcal vaccines were offered, age groups, prescription requirements, and how patient eligibility was determined. In addition, participants were asked to rate a series of patient-related and organizational barriers to pneumococcal vaccination. Results: Ninety-four pharmacies completed the survey, with most (96.8%) offering pneumococcal vaccines, most commonly PCV20 (95.6%). Most pharmacies vaccinated patients upon request (98.9%) or when patients presented with a prescription (82.4%), but few proactively contacted patients to schedule the vaccination (17.6%). Pharmacists most often administered pneumococcal vaccines to patients aged 65 and older and used patient age and immunization information systems to identify eligible patients. The most common patient-related barrier was the patient’s belief that they do not need the vaccine. The most common organizational barriers were inadequate reimbursements for vaccine administration and vaccine products. Conclusions: Pneumococcal vaccinations are commonly offered in rural community pharmacies, which play an important role in immunization access. With recent guideline changes to the age-based recommendation, there is an opportunity to optimize strategies to increase vaccine uptake.