Reading comprehension is a complex skill requiring both cognitive and motivational processes. Students with learning disabilities (LD) have more issues with reading comprehension than those without. It is therefore necessary to examine whether intrinsic motivation and other cognitive factors are also effective for students with LD. This study examines the extent to which the mediating effects of reading fluency, strategies or prior knowledge change the relationship between intrinsic motivation and reading comprehension in those both with and without LD. Participants of the research were 226 Turkish secondary school students, 113 with LD and 113 without. A multisample, parallel multiple mediation analysis was used to analyse the data. Findings were as follows: strategies and prior knowledge mediated the relationship between intrinsic motivation and reading comprehension in both groups, however, reading fluency was not mediated. The direct effects of the mediating variables did not differ between the groups and the direct effect of intrinsic motivation on reading comprehension was insignificant in both groups. These results show that a combination of interventions designed to increase intrinsic motivation and reading achievement is also beneficial for the reading comprehension of students with LD.