This study was a comparative investigation into the nature of difficulties and factors affecting the learning of English by the secondary school students of Provincial and Federal government schools in Khyber Pukhtunkhwa. The objectives of the study were (1)To measure the performance of secondary school students of Provincial and Federal government schools of Khyber Pukhtunkhwa in tenses, active and passives voices, direct and indirect narrations, conjunctions, prepositions, articles, construction of sentences and reading with comprehension; (2)To find out the level of difficulties of secondary school students of Provincial and Federal government schools of Khyber Pukhtunkhwa in tenses, active and passives voices, direct and indirect narrations, conjunctions, prepositions, articles, construction of sentences and reading with comprehension; (3)To compare the level of difficulties in learning English as a second language at secondary level of Provincial and Federal government schools in Khyber Pukhtunkhwa ; (4)To find out the factors affecting the learning of English at secondary level of Provincial and Federal government schools in Khyber Pukhtunkhwa); and (5)To provide a base for improvement of teaching English as a second language at the secondary level. The population of the study comprised of all the twenty four Provincial government schools and twenty two Federal government schools located in twenty four districts of Khyber Pukhtunkhwa. Six hundred and fifty four students were randomly selected from each systems of school by applying simple random sampling technique. Sixteen English teachers were selected by using purposive sampling technique for the purpose of interview An English language achievement test for secondary classes was administered to the sample students of the study and sample English teachers were interviewed. The data obtained were tabulated and analysed through SPSS 17.0 software to compute mean, standard deviation, t-value and p-value (significance) level. t-test was applied to measure the significance of difference between the means of both types of school systems. Significance was seen at .01 level as criterion for the rejection or acceptance of null hypothesis. The interview data was analyzed manually. The main findings of the study were; the students of Provincial government schools faced more difficulties in learning of verb forms, narration, conjunctions, prepositions, articles, sentence arrangements and reading comprehension. The students of both types of schools systems faced same difficulties in learning voices. The teachers in Provincial government schools were not sufficiently qualified and had no adequate knowledge of teaching methodologies of teaching English. The classes at both type of school system were overcrowded. The Provincial and Federal Government schools lacked audio-visual aids for teaching of English.