The national budget process is an important factor in a government’s ability to implement development plans. To that end, this paper analyses the budget cycle of national agricultural research institutes during 2001–11 in relation to their parent ministry, the Federal Ministry of Agriculture and Rural Development, with the objective of assessing the process in terms of critical elements of good governance, such as efficiency, effectiveness, transparency, and accountability. In theory, the budget process acts as a policy instrument to decouple the dual structure of the agricultural economy—which comprises both research and nonresearch components—with a view to improving the performance of the sector. Results indicate an increased preference for R&D during the period, accompanied by high degree of funding instability at the institutes. Agricultural research was emphasized much less in the the Ministry’s capital budget than in its recurrent budget. Furthermore, on average, the approved capital allocation to the institutes was higher than projected for the period, which in turn is higher than disbursed funding for the period. By comparison, the Ministry’s projected capital allocation was higher than was ultimately approved. The budget process was also fraught with considerable discrepancies and delays, coupled with an overt disconnect between planning and budgeting.