The effects of computer-based Working Memory (WM) training using two training procedures were examined among sixty-four primary-school children with Special Educational Needs (SEN). Measures of general cognitive ability, auditory and visuospatial working memory, arithmetic ability, and reading and writing skills were gathered and analysed. The referred group of SEN children predominantly had lower performance in auditory WM, arithmetics and reading and writing skills. The SEN children within respective school were randomized into either an active WM training group or a control group and ten schools participating in the WM training study were randomized into one of two different training conditions. At five schools the SEN children received regular WM training and at the other five schools the children received WM training with the addition of metacognitive strategy training. Results showed a significant difference in WM performance during training in favor of the metacognitive intervention. Furthermore, transfer effects occurred on visuospatial WM measures at posttest and at 6-month follow-up. Post-hoc tests showed that the effects pertained only to the metacognitive intervention. No transfer to arithmetic or reading and writing skills occurred after training in the two training conditions. Results were discussed in terms of metacognitive factors being important in optimizing performance in WM training, and that such factors should be taken into consideration when designing interventions for children with SEN. It is also suggested that in referral of children with SEN to remediation with WM training the WM profiles should be taken into consideration to a greater degree.