Background: Working memory problems have been targeted as core deficits in individuals with Fragile X syndrome (FXS); however, there have been few studies that have examined working memory in young boys with FXS, and even fewer studies that have studied the working memory performance of young boys with FXS across different degrees of complexity. The purpose of this study was to investigate the phonological loop and visual-spatial working memory in young boys with FXS, in comparison to mental age-matched typical boys, and to examine the impact of complexity of the working memory tasks on performance. Methods: The performance of young boys (7 to 13-years-old) with FXS (n = 40) was compared with that of mental age and race matched typically developing boys (n = 40) on measures designed to test the phonological loop and the visuospatial sketchpad across low, moderate and high degrees of complexity. Multivariate analyses were used to examine group differences across the specific working memory systems and degrees of complexity. Results: Results suggested that boys with FXS showed deficits in phonological loop and visual-spatial working memory tasks when compared with typically developing mental age-matched boys. For the boys with FXS, the phonological loop was significantly lower than the visual-spatial sketchpad; however, there was no significant difference in performance across the low, moderate and high degrees of complexity in the working memory tasks. Reverse tasks from both the phonological loop and visual-spatial sketchpad appeared to be the most challenging for both groups, but particularly for the boys with FXS. Conclusions: These findings implicate a generalised deficit in working memory in young boys with FXS, with a specific disproportionate impairment in the phonological loop. Given the lack of differentiation on the low versus high complexity tasks, simple span tasks may provide an adequate estimate of working memory until greater involvement of the central executive is achieved. (Contains 2 tables and 1 figure.)