Anogenital human papillomavirus (HPV) infection is the leading sexually transmitted infection in the United States. In October 2011, the quadrivalent HPV vaccine (HPV4) was recommended for males in the U.S. We analyzed a subsample of 11–26 year old (N = 1012) males, from the National Health and Nutritional Examination Survey 2011–2012 dataset, to examine HPV vaccine uptake. The initiation rates in the 11–17 years and the 18–26 years age-groups were 10.7% (95% confidence interval (CI): 8.09–16.6%) and 5.5% (95%CI: 3.1–9.5%) respectively. The corresponding HPV vaccine completion rates were 39.3% (16.7–67.7%) for the 11–17 year old males and 59.1% (37.2–77.6) for the 18–26-year-old males. Despite a slight increase, HPV vaccine uptake remained low among males. These findings can help in HPV vaccination policy in the United States, with a focus on informational messages directed toward young males and their parents in order to increase uptake of HPV vaccine.