This study explores the long-term effects of difficulties in reading and mathematical skills on educational achievement and successful graduation from secondary education as well as the role of special education in successful graduation. Study participants were all 16-year-old ninth graders from one Finnish city ( = 595; 302 females, 293 males) who were followed for 5 years after completing compulsory education. Students' reading and mathematical skills were measured at the end of compulsory education and their achieved grades in literacy and mathematics were received from their upper secondary schools. The overall results show that although part-time special education was available throughout both compulsory and upper secondary education, the negative longitudinal consequences of reading difficulties (RDs) and mathematical difficulties (MDs) on school achievement in literacy, mathematics, and rates of graduation can be seen. The regression path models were estimated separately for female and male students and show that among male students with RDs and MDs, the part-time special education that students received in Grades 7 to 9 was significantly related, but for Grades 10 to 11, this relationship is only significant among students with RDs. Moreover, low levels of school achievement in literacy among female students and in literacy and mathematics among male students significantly increased the likelihood of delayed graduation.