This paper addresses the issue of how to develop skill in operating cognitive tool for learning. Cognitive tool is an interactive application for encouraging learners to visualize/externalize the process or results of learning and to scaffold the learning process as modeled. Such scaffolding enables them to gain cognitive experience of the learning process. Although the learning skill development generally requires the learners to accumulate the cognitive experiences in operating the tool, it would not always induce them to reflect on how they operate it and on how they learn via the tool. Such reflection contributes to learning how to operate the tool, which also involves learning how to learn. In order to provide learners with an opportunity for reflection, this paper proposes fadable scaffolding with cognitive tool, in which functions available on the tool can be faded according to learning skill in a learner-adaptable way. Such fading enables learners not only to accomplish the learning process without the tool but also to gain a proper and deeper understanding of the functions to become more skillful in operating the tool. This paper demonstrates fadable scaffolding with Interactive History (IH for short) for developing skill in operating it, which is a cognitive tool for scaffolding navigation and knowledge construction process in hyperspace provided with unstructured and hypertext-based resources. We have conducted a case study with the fadable scaffolding with IH. The results suggest that the fadable scaffolding allows learners to fade the IH functions in a reasonable way and to become more skillful in operating IH, which would contribute to become more skillful in navigation and knowledge construction process.