The process by which funding organizations select among the myriad number of proposals they receive is a matter of significant concern for researchers and the public alike. Despite an extensive literature on the topic of peer review and publications on criteria by which clinical investigations are reviewed, publications analyzing peer review and other processes leading to government funding decisions on large multi-site clinical trials proposals are sparse. To partially address this gap, we reviewed the outcomes of scientific and programmatic evaluation for all letters of intent (LOIs) received by the Department of Veterans Affairs (VA) Cooperative Studies Program (CSP) between July 4, 2008, and November 28, 2016. If accepted, these LOIs represented initial steps towards later full proposals that also underwent scientific peer review. Twenty-two of 87 LOIs were ultimately funded and executed as CSP projects, for an overall success rate of 25%. Most proposals which received a negative decision did so prior to submission of a full proposal. Common reasons for negative scientific review of LOIs included investigator inexperience, perceived lack of major scientific impact, lack of preliminary data and flawed or confused experimental design, while the most common reasons for negative reviews of final proposals included questions of scientific impact and issues of study design, including outcome measures, randomization, and stratification. Completed projects have been published in high impact clinical journals. Findings highlight several factors leading to successfully obtaining funding support for clinical trials. While our analysis is restricted to trials proposed for CSP, the similarities in review processes with those employed by the National Institutes of Health and the Patient Centered Outcomes Research Institute suggest the possibility that they may also be important in a broader context.