Chemical immobilisation is an integral component for the conservation of wild animals and can be stressful if proper protocols are not administered. References on the immobilisation of Arabian striped hyaena (Hyaena hyaena sultana) are scarce. The current study was designed to evaluate the physiological and clinical responses of Arabian striped hyaena, immobilised with ketamine-medetomidine (KM) and ketamine-xylazine (KX); and to compare immobilisation effectiveness of the two combinations in a cross-sectional clinical study. A total of 15 (six males, nine females) (semi-) captive and adult Arabian striped hyaena with an average weight of 31.39 ± 0.36 kg were immobilised 50 times for annual vaccination and translocation purposes from January 2014 till March 2018 on Sir Bani Yas Island, United Arab Emirates. A total of 34 immobilisations were executed with (Mean ± SE) 2.27 ± 0.044 mg/kg ketamine and 0.04 ± 0.001 mg/kg medetomidine; while 16 with 4.95 ± 0.115 mg/kg ketamine and 0.99 ± 0.023 mg/kg xylazine. The drugs were remotely delivered intramuscular. The evaluation of physiological and clinical parameters included monitoring of vital signs through pulse oximetry, blood gas analysis of arterial blood through Istat blood gas analyser, and blood biochemistry and haematology. The quality of induction, anaesthesia and recovery was also assessed. Atipamezole (0.21 ± 0.003 mg/kg) was used to antagonise the effects of KM and 0.09 ± 0.003 mg/kg atipamezole or by 0.23 ± 0.006 mg/kg yohimbine for KX. Data were analysed using the general linear model and inferential statistics. KM was more effective in induction (scores; KM = 1.41 ± 0.10; KX = 1.31 ± 0.12), anaesthesia (KM = 1.00 ± 0.00; KX = 2.0 ± 0.0) and recovery (KM = 1.76 ± 0.15; KX = 2.69 ± 0.12) phases as compared to KX. There was a significant difference (P < 0.05) amongst the two combinations for anaesthesia time (KM = 59.5 ± 2.41; KX = 49.25 ± 1.31 min.), time to stand after reversal (KM = 4.91 ± 0.60; KX = 10.38 ± 1.48 min.) and full loss of the signs of anaesthetics (KM = 12.32 ± 1.37; KX = 21.25 ± 2.16 min.) along with rectal temperature (KM = 37.58 ± 0.29; KX = 36.00 ± 0.68 °C), pulse rate (KM = 50.46 ± 1.90; KX = 61.14 ± 2.79 beats/min), respiration rate (KM = 29.44 ± 0.99; KX = 23.80 ± 1.57 breaths/min.) and partial pressure of oxygen (KM = 89.59 ± 1.34; KX = 82.06 ± 3.92%). The blood oxygen saturation by oximeter indicated hypoxaemia in KX (82.06 ± 3.92), supported by the data from blood gas analyser. KM combination was more suitable for the immobilisation of Arabian striped hyaena, providing a better quality of induction, anaesthesia and recovery compared to KX. However, we strongly suggest further investigation to see the effects of oxygen supplementation for the compensation of hypoxaemia.