Ghana adopted the Integrated Disease Surveillance and Response (IDSR) system, which is an integration of the various programs in the surveillance system and can contain disease outbreaks and pandemics. Implementation of the IDSR is influenced by several factors which can affect its functionality and ability to contain disease outbreaks. This study assessed the factors influencing the IDSR system in selected districts in the Eastern Region of Ghana. A cross-sectional study was conducted between February-March, 2022 in Fanteakwa North, Abuakwa South and New Juaben South districts in the Eastern Region of Ghana among health care workers who are involved in IDRS activities. Both primary and secondary data were collected and analyzed using descriptive statistics and regression analysis at 0.05 significant level with 95% confidence interval. Three hundred and forty-seven (347) health care workers participated in the study with 56.2% (195/347) indicating that rumor registers were available at the health facilities. Most of the respondents (64.8%, 225/347) had means of transport for disease surveillance activities while majority (61.9%, 215/347) had case-based forms for case investigation. About half (51.9%, 180/347) of the participants revealed that they did not receive any feedback from the next higher level in the past year. Availability of transport for IDSR activities was almost 3.4 times more likely to contribute positively to IDSR system compared to facilities without transport (AOR = 3.36; 95% CI = 1.44-7.83; p = 0.005). Respondents who have the capacity to apply case definition are 2 times more likely to contribute to an effective IDSR system compared to health workers who cannot apply case definition (AOR = 1.94; 95% CI = 1.17-3.21; p = 0.013). Respondents who did not receive feedback from the next higher level were 52% less likely to have an effective IDSR system compared to respondents who received feedback from the next higher level (AOR = 0.48; 95% CI = 0.23-1.00; p = 0.05). Effective operation of IDSR is affected by the application of case definition and means of transport at health facilities. In addition, the capacity of health care workers to provide feedback can influence the smooth operation of the IDSR in the studied area in Ghana.