The purpose of this study was to explore the challenges facing pupils in learning English subject in public primary schools in Nyamagana District. The study applied mixed research approaches, both qualitative and quantitative. The researcher conducted the research in public primary schools whereby 5 out of 80 public primary schools were selected to represent the whole population in Nyamagana District. The study involved 186 pupils from standard three up to standard seven, 186 parents, 21 teachers, and 5 head teachers. Data was collected using questionnaires, interviews, focus group discussions and observation. Quantitative data was analyzed using descriptive analysis with the aid of SPSS (Statistical Package for Social Sciences) 20th version software and presented in form of tables using frequencies, percentages. The qualitative data was analyzed using thematic analysis and presented in quotation and narration form. The study revealed that pupils didn’t enjoy learning English subject, pupils do not understand English subject, and pupil’s ability to speak English language also pronunciation are the challenge facing pupils in learning English language as well as the communication language among pupils with their teachers is a challenge faced pupils in learning English language. Based on the findings and the conclusions drawn, the study recommend that teachers should guide and encourage pupils to perceive English language positively and seek more avenues where they can be practicing the language for better fluency and vocabulary development. Such avenues include socializing with other pupils from private schools who are fluent in the English language, overcoming the fear of making errors in speaking and writing English language and actively seeking help to correct errors and mistakes