Emergence of fault-tolerant quantum computers (FTQC) brings about promise of harnessing power of quantum computing at larger scale. At the same time, as quantum computers are expected to process more sensitive information, there is a need to understand the security issues in fault-tolerant quantum computers, and develop defenses for attacks that may compromise confidentiality or integrity of the data processed by FTQC. While noisy intermediate-scale quantum (NISQ) computers have already been studied from the security perspective, understanding security issues with FTQC is still an open research question. To address the missing research gap, this work presents the first exploration of possible security vulnerabilities of FTQC. The work presents analysis of possible threat models and outlines potential vulnerabilities of FTQC. Understanding the landscape of the threats can help lead to development of safer FTQC design at both software and hardware levels.