This chapter examines unprecedented challenges to academic freedom facing researchers at the intersection of artificial intelligence and neuroscience. While formal protections remain strong, actual research autonomy faces systematic erosion from multiple sources. This chapter documents how university administrators increasingly function as risk managers, constraining research through institutional oversight and anticipation of public backlash. Meanwhile, external funding agencies shape research directions through priority-setting that reflects political rather than purely scientific considerations. Perhaps most concerning is the widespread phenomenon of preemptive self-censorship, where researchers systematically avoid potentially valuable but controversial research directions before encountering formal limitations, creating “investigation deficits” where technical capability far exceeds actual research activity in sensitive domains. The analysis reveals significant regional variations in constraint patterns, with democratic societies experiencing “democratic constraints” through funding allocations and political oversight, while authoritarian contexts involve more direct intervention and strategic research alignment. AI neuroscience research faces distinctive vulnerabilities due to methodological complexity that enables public misunderstanding, dual-use concerns about potential military or surveillance applications, and expanding ethical review processes that extend beyond traditional participant protection. Through detailed case studies, this chapter illustrates how successful researchers develop sophisticated navigation strategies including “resilient research framing,” methodological rigor, strategic publication approaches, and proactive ethical engagement to maintain scientific inquiry while managing political pressures. This chapter concludes by advocating for “engaged academic freedom”—preserving essential scientific autonomy through sophisticated engagement with ethical and political concerns rather than isolation from them. This requires coordinated efforts at the individual, institutional, and systemic levels to maintain the freedom of inquiry essential to scientific progress while acknowledging legitimate societal concerns about increasingly powerful brain technologies.