Non-communicable diseases (NCDs) continue to pose threats to human health and development worldwide. Though preventable, NCDs kill more people annually than all other diseases combined. The four major NCDs namely cardiovascular diseases, chronic respiratory diseases, diabetes and cancers share common modifiable risk factors. In order to prevent and control NCDs, Ghana has adopted the World Health Organisation Package for Essential NCD (WHO-PEN) intervention, to be piloted in selected districts before a nationwide scale-up. We assessed the capacity of these facilities for the implementation of the WHO-PEN pilot. We conducted a cross-sectional health facility-based survey using a multistage sampling technique. We collected data on human resource, equipment, service utilization, medicines availability and health financing through interviews and observation. Descriptive data analysis was performed and expressed in frequencies and relative frequencies. In all, 23 health facilities comprising two regional hospitals, three district hospitals, nine health centres and nine Community-based Health Planning and Services (CHPS) compounds from three regions were surveyed. All the hospitals had medical officers whilst 4 (44.4%) of the health centres had physician assistants. Health financing is mainly by the National Health Insurance Scheme (NHIS). None of the health facilities had spacers and only one health centre had oxygen cylinder, glucometer and nebulizer. Gaps exist in the human resource capacity and service delivery at the primary care levels, the focus of WHO-PEN intervention. Adequately equipping the primary health care level with trained health workers, basic equipment, medications and diagnostics will optimize the performance of WHO-PEN intervention when implemented.