With an estimated 174 million in 2013, Nigeria is faced with innumerable challenges. One of such challenges is ensuring that public transit systems within its metropolitan areas are fast and effective. Our system of interest is the Bus Rapid Transit (BRT) system. This paper looks at the present challenges in deploying Electronic Fare Collection Systems for the Bus Rapid Transit (BRT) system in Lagos state, Nigeria. The study sampled commuters with questionnaires administered using a simple random sampling technique. The study also interviewed a representative of the Electronic Fare Collection System Technology Provider (e-Purse). Findings revealed commuters adoption of Electronic Fare Collection System remains low due to amongst other factors a lack of knowhow on the smart card usability. We propose an extended technical requirement for the Fare Collection system as well as modifications of the Lagos BRT policies that will ensure its effectiveness.