This study aimed to evaluate the effect of the summer pruning time in ‘Fuji’ apple trees on the quality of fruit at harvest and after storage in controlled atmosphere with extremely low O2 (CA-ELO) (0.5 kPa O2). The treatments evaluated were summer pruning in December, January, and February, in addition to a control treatment (without summer pruning). The experiment was carried out in the 2018/2019 and 2019/2020 growing seasons. The fruit were evaluated at harvest and after eight months of CA-ELO (0.5 kPa O2 + <0.5 kPa CO2/1.5 ± 0.2°C/92 ± 2% RH) storage, at chamber opening, and after 7 days of shelf-life at 23 ± 3°C and 60 ± 5% RH. The quality of the fruit was evaluated through of soluble solids, flesh firmness, titratable acidity, fruit color, and physiological disorder incidence (sunburn and flesh browning), in addition to enzymatic activity and concentration of functional compounds. There was no significant effect of the summer pruning time on fruit flesh firmness, soluble solids, titratable acidity, and rot incidence after storage under CA-ELO plus 7 days of shelf life. Summer pruning in February resulted in fruit with higher peel red color development, which in general contains a higher concentration of functional compounds at harvest (total phenolic compounds and total antioxidant activity), and lower flesh browning incidence in ‘Fuji’ apples stored under CA-ELO. The nitrogen (N) concentration and nitrogen/calcium ratio (N/Ca) in the second growing season were lower in fruit from plants pruned in February, compared to no summer pruning or earlier pruning. The superoxide dismutase and peroxidase enzyme activity were lower in fruit from treatments with summer pruning in January and February, whereas the polyphenol oxidase enzyme activity was lower when summer pruning was conducted in February.