Public Health Emergency Operations Center (PH-EOC) and Incident Management System (IMS) provides a platform for inter-sectoral coordination, and collaboration to enhance efficiency of response activities and help in effective control of disease outbreaks. Dengue fever (DF) is an emerging serious public health threat with a potential to transform into a public health emergency. Pakistan faced a heavy outbreak of Dengue fever (DF) from August to December 2019. National Institute of Health (NIH), Islamabad activated its Public Health Emergency Operations Center (PH-EOC) with an objective to implement principles and practices of IMS for control of the outbreak. The challenges during inter-sectoral collaboration for response activities were also identified. PH-EOC was activated on 16th September 2019, and remained operational for next 81 days till 05th December 2019. Incident management structure, incident action plan (IAP), and risk communication plan was developed and executed during this phase. Daily morning and evening meetings were held during all operational days. Federal and provincial health departments, district health offices (DHO), and government/private hospitals were coordinated for collection of the data pertaining to Dengue confirmed cases and deaths. As of 05th December 2019, a total of 52,877 confirmed Dengue cases were reported from all across Pakistan with maximum cases reported from Rawalpindi and Islamabad collectively i.e. 20,988 (40%), followed by Karachi 14,768 (28%), and Peshawar 2,699 (5%), while AJK reported 1,690 (3%). A total of 92 deaths happened all across Pakistan, out of which 43 (47%) happened in Karachi, 23 (25%) in Rawalpindi, and 22 (24%) in Islamabad. The response was coordinated through NIH based PH-EOC, but was carried out by relevant federal and provincial district health offices, vector surveillance programs, dengue control programs and sanitation departments respectively. As a part of response plan, vector surveillance, larva source management, and insecticidal spraying i.e. both fogging and indoor residual spraying activities were carried out in hotspots or the areas where confirmed cases were reported. Sanitation departments daily reported the removal of additional 80–100 ton of solid waste from hotspot areas. Hospitals were coordinated for reporting of isolation of DF patients and provision of quality clinical management for admitted patients. The International Federation for Red Cross/Crescent conducted community awareness, and covered 28,800 households in affected areas of Islamabad. Conversely, the DF outbreak was controlled 02-03 weeks ahead of previous years trends. All the coordinated activities were incorporated in a daily situation report (SitRep) and this was widely distributed among all the stakeholders through emails. Additionally, the data was displayed on the dashboard in PH-EOC. The data dashboard at PH-EOC served as an information management hub that visually mapped, tracked, analyzed, and displayed clusters of DF cases and hotspots. Accordingly, SitRep substantiated as the main reporting tool to monitor response activities initiated by rapid response teams at the national and subnational level. The inter-sectoral coordinating efforts made among concerned line departments resulted in a timely response leading to effective handling of a national public health threat. The information distilled from this experience was that the early and judicious activation of PH-EOC with adaptation of IMS under decision making leadership resulted in a well-managed and prompt response executed by different departments/stakeholders, and effective control of the outbreak before its transformation into a public health event/emergency of national or international concern.