This study examined the initiation and logistics, funding, perceived barriers and benefits, and disruption of school activities by school-located influenza vaccination (SLIV) programs conducted during the 2008-2009 influenza season. Seventy-two interviews using a structured protocol were conducted with 26 teachers, 16 school administrators, and 30 health care professionals from 34 schools in 8 school districts. SLIV programs used a variety of locations, scheduling and staffing options, and methods for receiving parental consent and screening children. Health care professionals were primarily responsible for implementing SLIV programs, and most administrators and health care professionals considered programs easy to initiate. Health care professionals identified successful programs as requiring adequate planning/coordination, a dedicated program coordinator, and a consistent funding source. Most respondents (96%) reported minimal school-day disruptions. The perception of most stakeholders is that SLIV programs can be relatively easy to initiate, minimally disruptive and can become more efficient with experience, especially with feedback from all stakeholders.