Since the early years, children with learning disabilities were enrolled in special schools and this led to their segregation from regular schools. They were basically looked down upon in the society. Today the government and key educational stakeholders have put great efforts in trying to include these learners into mainstream schools where they learn with the regular pupils. This has not been successful since not all children with special learning needs and who have attained the school age are enrolled in schools. This formed a basis for the researchers‟ topic in trying to unearth challenges faced in the implementation of Special Needs Education (SNE) in public primary schools in Nyeri town and the barriers to total success of the programme. The purpose of the study was to establish the challenges faced in the implementation of SNE in Nyeri town. It sought to provide valuable information on the challenges to educational planners and other stakeholders and suggest curative measures and recommendations to curb the problem. This study was based on the classical theory of equal opportunities advanced by Sherman and Wood (1982). The objectives of the study were:-To find out the status of implementation of SNE in Nyeri town, to determine the availability of teaching-learning resources in schools offering the SNE programme, to assess teacher preparedness to undertake the SNE curriculum implementation and to analyze barriers and give responses to these challenges. The study adopted the descriptive survey design in collecting data in order to answer the outlined objectives and the research questions it set out to achieve. The proposed study was carried out among teachers, head teachers and education ministry officials. The target population was the 42 public primary schools, 42 head teachers, 538 primary school teachers and 40 ministry officials. The study sample included all the 5 public primary schools offering special education and those with special units, 7 regular schools randomly sampled making a total of 12 schools. From the 12 schools, the 12 head teachers were all chosen, 60 teachers five from each sampled school, 8 area educational officers giving a total of 80 respondents. The research instruments used were:-observation checklists, questionnaires, interview schedules and document analysis. The analysis done was both qualitative and quantitative. Qualitative analysis considered the conclusions from the respondents‟ opinions. Quantitative analysis involved use of frequency counts and distribution, tabulation, totals and calculation of percentages aimed at condensing the data collected into meaningful groups and tables for further analysis. Data collected was analyzed using statistical package for social sciences (SPSS) and was presented in form of graphs, percentages, tables and charts. The study found out that SNE implementation in public primary schools in Nyeri town, Nyeri County was faced by numerous challenges and the most prominent challenges are sociocultural, geographical, parental and school-based factors. Socio-economic factors played minimal role as an SNE barrier. This calls for concerted efforts between key educational stakeholders to conduct aggressive campaigns to sensitize the public on importance of the SNE programme. The government should increase funding to SNE. More teachers be trained and schools provided with adequate resources. Educational policies should be aligned to SNE. Curriculum for the special pupils should be provided and parentsteachers collaboration encouraged. In conclusion, further research needs to be carried out in the following areas; similar studies in public secondary schools, more research in the same county but in a different locale as well as other counties in Kenya and further research on possible hidden factors not revealed by this study.