<p>This study examines research productivity and novelty under different funding mechanisms of the National Institute of Health (NIH). We analyze two layers of funding relationships: (1) intramural versus extramural funding, comparing stable and competitive funding models, and (2) project grants versus cooperative agreements within extramural funding, assessing human capital input and financial investment. Our findings show that competitive extramural funding is associated with higher publication volumes, while stable intramural funding is linked to outputs with greater novelty. Within extramural mechanisms, cooperative agreements are associated with more publications than project grants, primarily due to larger collaborative group sizes rather than increased financial input. However, cooperative agreements are linked to lower research novelty, largely due to greater financial investment. These results highlight the importance of aligning human and financial resources to optimize research outcomes. A balanced approach between intramural and extramural funding mechanisms can support both productivity and innovation.</p>