English is the first official language in Uganda and it is learnt as a second language (L2) in the country. The language-in-education policy allows for the teaching of English as subject for the first three years in rural schools before it is initiated as a language of learning and teaching (LoLT) from the fourth year onwards. Urban schools use this language as LoLT right from P.1 because of the assumed complex multilingualism in these schools. This paper draws from a wider PhD study in progress which focuses on how teachers understand and manage the process of transition from mother tongue (MT) education to English medium education in Uganda. Data for this study was collected by manner of questionnaires, classroom observations and interviews from ten schools in Uganda. This paper reports on the challenges of teaching and learning English in multilingual rural schools in Uganda. The data reported here was collected in two private and two public (primary) schools in Rakai district. The preliminary findings in this study reveal that the challenges of teaching and learning of English range from a disjointed policy implementation, teacher training, availability of materials, the nature of the curriculum and teachers’ perceptions towards learning English. The evidence in this study suggests a need of educating both teachers and the public in Uganda on possible ways of learning English. In addition, the pedagogical implications of these findings to the transition to English in Uganda are discussed.