Efficient management and control of government's cash resources rely on government banking arrangements. Nigeria, like many low income countries, employed fragmented systems in handling government receipts and payments. Later in 2016, Nigeria implemented a unified structure as recommended by the IMF, where all government funds are collected in one account would reduce borrowing costs, extend credit and improve government's fiscal policy among other benefits to government. This situation motivated us to embark on this research to design and implement an integrated system for vehicle clearance and registration. This system complies with the new Treasury Single Account policy to enable proper interaction and collaboration among five different level agencies (NCS, FRSC, SBIR, VIO and NPF) saddled with vehicular administration and activities in Nigeria. Since the system is web based, Object Oriented Hypermedia Design Methodology (OOHDM) is used. Tools such as Php, JavaScript, css, html, AJAX and other web development technologies were used. The result is a web based system that gives proper information about a vehicle starting from the exact date of importation to registration and renewal of licensing. Vehicle owner information, custom duty information, plate number registration details, etc. will also be efficiently retrieved from the system by any of the agencies without contacting the other agency at any point in time. Also number plate will no longer be the only means of vehicle identification as it is presently the case in Nigeria, because the unified system will automatically generate and assigned a Unique Vehicle Identification Pin Number (UVIPN) on payment of duty in the system to the vehicle and the UVIPN will be linked to the various agencies in the management information system.