Background: Our aim was to investigate the relationship between the number of stroke physicians (SPs) and management of intravenous thrombolysis using recombinant tissue plasminogen activator (IV rt-PA) in Japan. Methods: Questionnaires about the infrastructure of acute-stroke care were sent to 1,466 hospitals that treated acute-stroke patients in September 2007. The responses were categorized as follows: (1) established or ineligible for IV rt-PA before September 2007, and discontinued or starting IV rt-PA from October 2007 to September 2008; (2) total number of SPs in those hospitals; (3) infrastructures according to acute-stroke treatment. Components related to discontinuing or starting IV rt-PA were analyzed. Results: Responses were received from 1,025 hospitals. Of these, 950 hospitals were continuing administration to acute-stroke patients, but 75 had discontinued administration. Before September 2007, 466 hospitals had already established administration of IV rt-PA (rt-PA hospitals) after government approval of IV rt-PA (non-rt-PA hospitals). From October 2007 to September 2008, 45 of 466 rt-PA hospitals (9.7%) discontinued IV rt-PA, while 29 of 479 (6.1%) non-rt-PA hospitals started. Less than 3 SPs were present in 73.9% of the 45 discontinued IV rt-PA hospitals and 37.9% of the 29 starting hospitals. In multivariate analysis, discontinuing IV rt-PA was inversely associated with ≥3 SPs (odds ratio = 0.37; 95% confidence interval = 0.15–0.87; p = 0.023). Factors associated with starting IV rt-PA were ≥3 SPs (OR = 6.19; 95% CI = 2.01–19.08; p = 0.002). Conclusions: The number of SPs available may contribute to the management of rt-PA hospitals.