This study employed the design-based research (DBR) methodology to explore how to design instructional prompts integrated into a computer-based cognitive tool, GeoGebra, for gifted mathematics education. This study was divided into two iterative research phases lasting for 3 semesters, in which differentiating the instructional prompts for gifted students was explored. During two iterations, a combination of quantitative and qualitative data collection and analysis procedures were used to examine the effect of the designed prompts on gifted students' learning achievements and explore their feedback on the learning activities based on the research conducted on 60 participants who were tenth-grade students. The findings led to a set of design propositions that contribute to the literature on both instructional prompts integrated into computer-based cognitive tools and gifted mathematics education. The propositions emphasize: (1) prompts' types, the algebraic-based prompts (ABPs) and software-based prompts (SBPs); (2) prompts' order, emphasizing on presenting ABPs before SBPs; (3) prompts' sequencing, adjusting the number of prompts' sequences to gifted students' characteristics; and (4) prompts' combination, merging ABPs and SBPs to gain higher order learning outcomes. The prospective studies for the next phases of the DBR study are also discussed.