Abstract Background Public health emergencies have the potential to disproportionately impact disadvantaged populations due to pre-established social and economic inequalities. Internationally, prior to the 2009 H1N1 influenza pandemic, existing pandemic plans were created with limited public consultation; therefore, the unique needs and characteristics of some First Nations communities may not be ethically and adequately addressed. Engaging the public in pandemic planning can provide vital information regarding local values and beliefs that may ultimately lead to increased acceptability, feasibility, and implementation of pandemic plans. Thus, the objective of the present study was to elicit and address First Nations community members’ suggested modifications to their community-level pandemic plans after the 2009 H1N1 influenza pandemic. Methods The study area included three remote and isolated First Nations communities located in sub-arctic Ontario, Canada. A community-based participatory approach and community engagement process (i.e., semi-directed interviews (n = 13), unstructured interviews (n = 4), and meetings (n = 27)) were employed. Participants were purposively sampled and represented various community stakeholders (e.g., local government, health care, clergy, education, etc.) involved in the community’s pandemic response. Collected data were manually transcribed and coded using deductive and inductive thematic analysis. The data subsequently informed the modification of the community-level pandemic plans. Results The primary modifications incorporated in the community-level pandemic plans involved adding community-specific detail. For example, ‘supplies’ emerged as an additional category of pandemic preparedness and response, since including details about supplies and resources was important due to the geographical remoteness of the study communities. Furthermore, it was important to add details of how, when, where, and who was responsible for implementing recommendations outlined in the pandemic plans. Additionally, the roles and responsibilities of the involved organizations were further clarified. Conclusions Our results illustrate the importance of engaging the public, especially First Nations, in pandemic planning to address local perspectives. The community engagement process used was successful in incorporating community-based input to create up-to-date and culturally-appropriate community-level pandemic plans. Since these pandemic plans are dynamic in nature, we recommend that the plans are continuously updated to address the communities’ evolving needs. It is hoped that these modified plans will lead to an improved pandemic response capacity and health outcomes, during the next public health emergency, for these remote and isolated First Nations communities. Furthermore, the suggested modifications presented in this paper may help inform updates to the community-level pandemic plans of other similar communities.