The Vaccines for Children (VFC) program distributes one half of all vaccines administered to US children. Compared with commercial vaccine distribution, VFC distribution is more complex. This prospective observational study compares the delivery and administration of VFC versus non-VFC influenza vaccine in US pediatricians' offices across 3 influenza seasons and its apparent impact on 2-dose compliance rates. Because of earlier shipping (mean = 29-42 days) of non-VFC vaccines, administration of VFC vaccines was delayed relative to non-VFC vaccines by approximately 1 month in 2007-2008 and 2008-2009 and 2 weeks in 2010-2011. Two-dose compliance rates for the VFC and non-VFC populations were 38.5% and 47.5% (P < .001) in 2007-2008, 45.9% and 55.1% (P < .001) in 2008-2009, and 50.0% and 52.9% (P < .001) in 2010-2011, respectively. Despite delays, earlier VFC shipment in 2010-2011 enabled greater equity in 2-dose compliance.