The main methods of apple tree recovery from latent viruses are thermotherapy and chemotherapy. Depending on the type of virus, the applied methods of apple tree recovery can be different and require improvement in relation to the biological characteristics of the rootstock 62–396 and the properties of viruses. The aim of the research is to study the features of recovery from the main harmful viruses of the apple tree clonal rootstock 62–396 using the methods of complex in vitro therapy. The recovery of plants of t apple tree clonal rootstock 62–396 from the ACLSV, ApMV and ASGV viruses was carried out in 2021–2022 using antiviral drugs (AVD) of ribavirin (standard) 40 mg/L, phenolcarboxylic acid 30 mg/L and cyclopentanone 2.5 mg/L at air temperatures +20°C and +38°C. Thermotherapy of explants at a temperature of +38°C was carried out in the KS-200 SPU climatostat for three months. Magnetic pulse processing (MPР) was carried out using the AMIS-8 device. At a temperature of +20°C, the possibility of using AVD for 45 and 90 days was established. The combination of AVD with a temperature of +38°C for 45 days resulted in relatively high parameters of explant survival rate, while increasing of duration to 90 days led to a 1.7-fold decrease in survival rate. The combination of temperature +38°C and MPР (without AVD), temperature +38°C and phenolcarboxylic acid provided a high survival rate of 81.3%. The combination of a temperature of +38°C and ribavirin, a temperature of +38°C and ribavirin plus MPР, a temperature of +38°C with phenolcarboxylic acid plus cyclopentanone provided an average survival rate of 56.3%. Growth parameters in apple rootstock 62–396 explants depended on the type of AVD, temperature, and MPР. Application of the studied AVD at a temperature of +20°C after 1.5 months of cultivation resulted in a 2.1–3.2-fold decrease in the number of shoots compared to the control. Increasing the temperature to +38°C inhibited the formation of shoots in all variants, leading to a 2.9-fold decrease in the number of shoots in the control, and a 1.1–1.5-fold decrease in the variants with AVD. Treatment with magnetic induction pulses reduced the inhibitory effect of high temperature in the control. The yield of latent virus-free explants of apple tree clonal rootstock 62–396 in vitro by different methods of rehabilitation was 50%. A low virus infection index (1.2 for ACLSV and ASGV, 1.6 for ApMV) was observed during the complex therapy using AVD (phenolcarboxylic acid + cyclopentanone), thermal and magnetic therapy.