Working conditions of High-performance Marine Craft (HPMC) occupants are inherent with shock and vibration. Therefore, HPMC occupants are usually investigated believing that their psychophysical health and performance are negatively affected by exposure to these conditions. However, the association between the regular occupational vibration exposures of HPMC occupants and the deterioration of their health and performance is disputable. Therefore, a sample of HPMC occupants are investigated in a prospective cohort study by measuring perceived work exposure, health and performance via validated web-based questionnaires and physical work exposure as vibration using measurement systems installed onboard their craft. Incidence of musculoskeletal pain (MSP) during four operational seasons is determined and presented as incidence proportion (IP). Association between accumulated vibration exposure aboard HPMC and incidence of MSP is systematically assessed using multiple logistic regression models and expressed as odds ratio (OR). Moreover, the correlation between objectively and subjectively measured vibration exposures is determined using the Spearman’s rank correlation coefficient (rs). Incidence proportion of neck pain was 63.4% and that of lower back pain ranged from 12.5% to 87.5% over the four seasons. The accumulated vibration exposure was strongly associated with the incidence of MSP primarily with lower back pain. However, the association was not statistically significant. The objective and subjective vibration exposures of the craft drivers showed a statistically significant positive monotonic correlation. The study suggests that occupational exposure to shock and vibration aboard HPMC is a factor increasing the incidence of MSP. The HPMC occupants regularly experience attrition in their performance. The perceived vibration exposure of the drivers can be used to rank the exposure severity aboard HPMC in the absence of objective measurements. The current vibration exposure assessment methods are also recommended to be revised accounting for shock and vibration inherent in HPMC exposures.