Anti-vaccination sentiment exists worldwide and Japan is no exception. Health professionals publish pro-influenza vaccination messages online to encourage proactive seeking of influenza vaccination. However, influenza vaccine coverage among the Japanese population is less than optimal. The contents of pro- and anti-influenza vaccination websites may contribute to readers’ acceptance of one or the other position. We aimed to use a text-mining method to examine frequently appearing content on websites for and against influenza vaccination. We conducted online searches in January 2017 using two major Japanese search engines (Google Japan and Yahoo! Japan). Targeted websites were classified as ‘pro’, ‘anti’ or ‘neutral’ depending on their claims, with author(s) classified as ‘health professionals’, ‘mass media’ or ‘laypersons’. Text-mining analysis was conducted, and statistical analysis was performed using a chi-squared test. Of the 334 websites analyzed, 13 content topics were identified. The three most frequently appearing content topics on pro-vaccination websites were vaccination effect for preventing serious cases of influenza, side effects of vaccination, and efficacy rate of vaccination. The three most frequent topics on anti-vaccination websites were ineffectiveness of influenza vaccination, toxicity of vaccination, and side effects of vaccination. The main disseminators of each topic, by author classification, were also revealed. We discuss possible tactics of online influenza vaccination promotion to counter anti-vaccination websites.