Nigeria’s Public Procurement Act 2007 was a response to the World Bank’s assessment of Nigeria’s Public Procurement system in 1999. The assessment revealed weaknesses in the system which called for urgent reforms. The Country`s Procurement Assessment Report (CPAR) showed that Nigeria’s public procurement system was without a legal framework, hence the setbacks. This paper investigates the impact of the Public Procurement Act 2007 on the functions of the governing councils of federal universities in Nigeria, applying the doctrinal research methodology. The study finds that there was another federal legislation: Universities (Miscellaneous Provision) Act No 11 of 1993 (as Amended) that established the federal universities’ governing councils and vested in them the authority to run these universities. The powers of the vice chancellors under the Public Procurement Act 2007 overlap with the functions of the governing councils under the extant 1993 Act. While the later Act made the Vice Chancellor the accounting officer with special responsibilities on issues relating to procurement, it was silent on the level of authority that the governing councils could exert on the universities. The paper also finds some merits and demerits of the Public Procurement Act 2007 in federal universities and concludes that there are still weaknesses in the enforcement and enforceability of the Act. It recommended chiefly, an amendment of the Public Procurement Act 2007 together with the Universities (Miscellaneous Provisions) Act 1993 to resolve the overlapping mandates.