A common yet untested assumption of cognitive training in children is that activities should be adaptive, with difficulty adjusted to the individual's performance in order to maximize improvements on untrained tasks (known as transfer). Working memory training provides the ideal testbed to systematically examine this assumption as it is one of the most widely studied domains in the cognitive training literature, and is critical for children's learning, including following instructions and reasoning. This trial aimed to examine children's outcomes of working memory training using adaptive, self-select (child selects difficulty level), and stepwise (difficulty level increases incrementally) approaches to setting the difficulty of training activities compared to an active control condition immediately and 6-month postintervention. While the aim is exploratory, we hypothesized that children allocated to a working memory training condition would show greater improvements: (1) on near transfer measures compared to intermediate and far transfer measures and (2) immediately postintervention compared to 6-month postintervention. This double-blinded, active-controlled, parallel-group randomized trial aimed to recruit 128 children aged 7 to 11 years from 1 metropolitan primary school in Melbourne, Australia. Following baseline testing, children were randomized into 1 of 4 conditions: adaptive, self-select, or stepwise working memory training, or active control. An experimental intervention embedded in Minecraft was developed for teachers to deliver in class over 2 consecutive weeks (10 × 20-minute sessions). The working memory training comprised 2 training activities with processing demands similar to daily activities: backward span and following instructions. The control comprised creative activities. Pre- and postintervention, children completed a set of working memory tests (near and intermediate transfer) and the Raven's Standard Progressive Matrices (far transfer) to determine training outcomes, as well as motivation questionnaires to determine if motivations toward learning and the intervention were similar across conditions. Caregivers completed the ADHD-Rating Scale-5 to measure their child's attention (far transfer). Statistical analysis will include traditional null hypothesis significance testing and Bayesian methods to quantify evidence for both the null and alternative hypotheses. Data collection concluded in December 2022. Data are currently being processed and analyzed. This trial will determine whether the adaptive approach to setting the difficulty of training activities maximizes cognitive training outcomes for children. This trial has several strengths: it adopts best practices for cognitive training studies (design, methods, and analysis plan); uses a range of measures to detect discrete levels of transfer; has a 6-month postintervention assessment; is appropriately powered; and uses an experimental working memory training intervention based on our current understanding of the cognitive mechanisms of training. Findings will inform future research and design of cognitive training interventions and highlight the value of the evidence-based principles of cognitive training. Australian New Zealand Clinical Trials Registry, ACTRN12621000990820; https://www.anzctr.org.au/ACTRN12621000990820.aspx. DERR1-10.2196/47496.