During the H1N1 outbreak of 2009, local public health units engaged in consultations with various levels of government to develop clinical practice guidelines. These guidelines provide specific clinical considerations around prevention, management, and treatment associated with the particular pathogen involved and are used by frontline healthcare professionals across many healthcare settings. In this article, we report on the lessons learned by Medical Officers of Health from across Canada on the guideline development and deployment processes and provide suggestions to improve guidelines development and deployment during future pandemic situations.