The importance of pharmacovigilance (PV) in ensuring drug safety, especially in the detection and prevention of adverse drug reactions (ADRs) is critical. However, PV activities in Nigeria still face many challenges, such as very low spontaneous reporting rates, and inadequate training and funding. This study assessed the state of pharmacovigilance in the federal capital territory of Nigeria (FCT), using WHO pharmacovigilance indicators. A cross-sectional questionnaire-based survey was carried out among secondary healthcare facilities in the FCT. The WHO Pharmacovigilance Indicators Questionnaire, which consists of the structural, process and outcome measures, was used to collect data from the focal person for pharmacovigilance at all the consenting facilities. Descriptive statistics were used to summarize all variables. Ethical approval was obtained from the Ethics Review Committee of the FCT development authority. Of the 14 secondary healthcare facilities in the FCT, 11 agreed to the study (response rate = 84.6%). Among the respondents, 4 (36.4%) were females, and 2 (18.2%) had 9 years of experience in pharmacovigilance. For the core structural indicators, 7 (63.6%) of the facilities had a pharmacovigilance center while only 4 (36.4%) had a copy of the Nigerian pharmacovigilance policy. Regarding financial provisions, 10 (90.9%) hospitals reported that there was no regular financial provision for the center while 10 (90.9%) centers had a standard adverse drug reaction reporting form. For the core process indicators, the mean ± SD of the nine core process indicators ranged from 0.9 ± 3.0 to 75.6 ± 38.6 and the total number of reports in the local database, therapeutic ineffectiveness, and medication error were limited. The assessment of pharmacovigilance activities in the Federal Capital Territory of Nigeria revealed significant gaps in infrastructure, financial support, and process implementation. Despite the presence of pharmacovigilance centers in the majority of facilities, the lack of consistent financial support and limited adherence to core process indicators highlight the need for enhanced training, resources, and policy enforcement to improve ADR reporting and overall drug safety monitoring. Strengthening these areas is crucial for advancing pharmacovigilance practices and ensuring patient safety in Nigeria.