Zebrafish are frequently used as a means to investigate development. These studies increasingly require repeated anaesthesia of zebrafish during juvenile (i.e. metamorphic) stages. The effects of anaesthesia during this time remain poorly studied. The aim of this study was to develop a reliable method that can be used for frequently repeated anaesthesia during juvenile stages. Initially, we assessed different concentrations of MS-222, the most commonly used fish anaesthetic, for 30 minute anaesthesia with recovery. We showed that suitable MS-222 doses could be identified for the smallest (7mm) and largest (20mm) fish. However, we found that juvenile fish within a specific metamorphic window (sized between 8-16 mm) were vulnerable to MS-222 and no standard concentration of MS-222 provided reliable anaesthesia under these conditions. Hence we focussed our efforts on identifying a protocol for these stages. We tested six different published anaesthesia protocols P1-P6 where P1, P2 corresponds to 0.01% MS-222, P3, P4: 0.085% 2-phenoxyethanol and P5, P6: 0.00025%/0.0050% Propofol/Lidocaine. In protocols P1, P3, P5 fish were maintained by immersion, whilst in P2, P4 and P6: fish were maintained on an anaesthetic-doused cotton-pad. We assessed reliable anaesthesia using 10 fish for 10 minutes, with full recovery. Our data allowed us to eliminate two of these protocols as unsuitable for short term anaesthesia with recovery of juvenile fish. Extending these studies to explore repeated anaesthesia at 4 day intervals for 20 days under the remaining four protocols, we showed that P1 and P4 were both suitable for repeated anaesthesia, and that P4 was most suitable for imaging. We confirmed that P4 remained suitable when the frequency of anaesthesia was increased to every 2 days. We conclude that this protocol provides a refinement to the current protocol for repeated anaesthesia with recovery of juvenile zebrafish in the vulnerable metamorphic window.