Auditory processing disorder (APD) is defined as a specific deficit in the processing of auditory information along the central auditory nervous system, including bottom-up and top-down neural connectivity. Even though music comprises a big part of audition, testing music perception in APD population has not yet gained wide attention in research. This work tests the hypothesis that deficits in rhythm perception occur in a group of subjects with APD. The primary focus of this study is to measure perception of a simple auditory rhythm, i.e., short isochronous sequences of beats, in APD children and to compare their performance to age-matched normal controls. The secondary question is to study the relationship between cognition and auditory processing of rhythm perception. We tested 39 APD children and 25 control children aged between 6 and 12 years via (a) clinical APD tests, including a monaural speech in noise test, (b) isochrony task, a test measuring the detection of small deviations from perfect isochrony in a isochronous beats sequence, and (c) two cognitive tests (auditory memory and auditory attention). APD children scored worse in isochrony task compared to the age-matched control group. In the APD group, neither measure of cognition (attention nor memory) correlated with performance in isochrony task. Left (but not right) speech in noise performance correlated with performance in isochrony task. In the control group a large correlation ( = -0.701, = 0.001) was observed between isochrony task and attention, but not with memory. The results demonstrate a deficit in the perception of regularly timed sequences in APD that is relevant to the perception of speech in noise, a ubiquitous complaint in this condition. Our results suggest (a) the existence of a non-attention related rhythm perception deficit in APD children and (b) differential effects of attention on task performance in normal vs. APD children. The potential beneficial use of music/rhythm training for rehabilitation purposes in APD children would need to be explored.