Auditing has been a major player in the development in the growing economies across the world. Audit is the examination of financial statements on an organization or institution on behalf of the users of the statements with an aim to detect fraud and errors. NG-CDF was formed by the Act of parliament in 2003 and amended in 2007, 2015 and 2016 to bring about socio- economic development of the people at the constituencies level in order to reduce poverty and enhance regional equity and they are audited to ensure accountability. The researcher therefore examined the challenges affecting auditing of NG-CDF projects in public schools in Homa Bay town constituency. The threats to the auditor’s independence and the loss of assurance by stakeholders in the ability of a financial statements audit to ensure accountability in the stewardship of the NG-CDF projects in public schools in Homa Bay town constituency raises questions on whether audits are relevant. It is in this context that this study was carried out. Literature was reviewed as per the objectives of the study, both general objectives and specific objectives. This research used descriptive survey method. The research used questionnaires to collect information and the data has been collected from Homa Bay town constituency. The findings were analyzed and conclusions and recommendations given.