The aim of this study was to monitor acute response patterns of autonomic and central nervous system activity during an encounter with Antarctica by synchronously recording heart rate variability (HRV) and electroencephalography (EEG). On three different time-points during the two-week sea journey, the EEG and HRV were recorded from nine male scientists who participated in "The First Turkish Antarctic Research Expedition". The recordings were performed in a relaxed state with the eyes open, eyes closed, and during a space quantity perception test. For the EEG recordings, the wireless 14 channel EPOC-Emotiv device was used, and for the HRV recordings, a Polar heart rate monitor S810i was used. The HRV data were analyzed by time/frequency domain parameters and ordinal pattern statistics. For the EEG data, spectral band power in the conventional frequency bands, as well as permutation entropy values were calculated. Regarding HRV, neither conventional nor permutation entropy calculations produced significant differences for the different journey time-points, but only permutation entropy was able to differentiate between the testing conditions. During the cognitive test, permutation entropy values increased significantly, whereas the conventional HRV parameters did not show any significant differences. In the EEG analysis, the ordinal pattern statistics revealed significant transitions in the course of the sea voyage as permutation entropy values decreased, whereas spectral band power analysis could not detect any significant difference. Permutation entropy analysis was further able to differentiate between the three testing conditions as well between the brain regions. In the conventional spectral band power analysis, alpha band power could separate the three testing conditions and brain regions, and beta band power could only do so for the brain regions. This superiority of permutation entropy in discerning subtle differences in the autonomic and central nervous system's responses to an overwhelming subjective experience renders it suitable as an analysis tool for biomonitoring in extreme environments.