Virtual reality (VR) can enrich neuropsychological testing, yet the ergonomic trade-offs of its input modes remain under-examined. Seventy-seven healthy volunteers—young (19–29 y) and middle-aged (27–56 y)—completed a VR Trail-Making Test with three pointing methods: eye-tracking, head-gaze, and a six-degree-of-freedom hand controller. Completion time, spatial accuracy, and error counts for the simple (Trail A) and alternating (Trail B) sequences were analysed in 3 × 2 × 2 mixed-model ANOVAs; post-trial scales captured usability (SUS), user experience (UEQ-S), and acceptability. Age dominated behaviour: younger adults were reliably faster, more precise, and less error-prone. Against this backdrop, input modality mattered. Eye-tracking yielded the best spatial accuracy and shortened Trail A time relative to manual control; head-gaze matched eye-tracking on Trail A speed and became the quickest, least error-prone option on Trail B. Controllers lagged on every metric. Subjective ratings were high across the board, with only a small usability dip in middle-aged low-gamers. Overall, gaze-based ray-casting clearly outperformed manual pointing, but optimal choice depended on task demands: eye-tracking maximised spatial precision, whereas head-gaze offered calibration-free enhanced speed and error-avoidance under heavier cognitive load. TMT-VR appears to be accurate, engaging, and ergonomically adaptable assessment, yet it requires age-specific–stratified norms.