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The promotion of health research, including the topic of physical activity (PA), is a constitutional responsibility of the Brazilian Unified Health System (SUS). This study aimed to: a) analyze the temporal trends and regional distribution of the number and amount of funding allocated to PA related research; and b) b) identify the funding modalities of these research projects financed by the Ministry of Health. This is an ecological study based on data from the Health Research System, covering the period from 2002 to 2023. Differences were observed in the number of funded studies and the deflated total investment across funding modalities, National Health Plan (PNS) periods, and macro-regions. The Research Program for SUS (PPSUS) was the funding modality that supported the highest number of studies, while national-level funding accounted for the largest share of financial resources. The highest number of studies was recorded during the 2004–2007 PNS, whereas the greatest volume of resources was allocated during the 2008–2011 PNS. Regional disparities in PA research funding were evident: the South region had the highest number of studies—both in absolute terms and per capita—as well as the highest research funding rate, while the Southeast received the largest share of financial resources. There is a need to expand and promote a more equitable distribution of funding for PA research, particularly through PPSUS.