The release of new apple varieties able to improve consumer satisfaction provides the opportunity to modernize orchards and transition them away from unlucrative plantings towards highly productive, high-value cultivation systems. Top-working an existing, unprofitable mature orchard by grafting a new variety allows the orchardist to take advantage of an existing root system to achieve early bearing and reduce the establishment cost. Often, the scion in a new top-grafted orchard can present excessive vigor in the years following the grafting due to the abundance of reserves stored in the mature root system that become available for the new variety at the beginning of the season. This case study focuses on ‘WA 38′, an apple variety released in 2017 to Washington State growers. ‘WA 38′ can show variable vigor levels depending on the choice of rootstock, training system, planting density, pruning technique, water availability, and soil characteristics. Prohexadione-calcium (Pro-Ca, Apogee®) has been utilized for years in apple and other crops as a growth regulator with inhibitory activity on gibberellin synthesis, with the common effect of reducing shoot growth and canopy development and other potential physiological effects depending on genetics of the variety, timing, and rate of applications. This study investigated the physiological responses of ‘WA 38′ scion top-grafted on an 8-year-old Granny Smith/M.9 orchard and then trained to 1, 2, and 3-axis systems—suitable for modern mid-high-density planting—with and without the application of Pro-Ca for two consecutive years. The growth regulator was applied in post-bloom at a 250 ppm rate, starting at approximately 12-cm shoot length for three sprays per season. The parameters assessed to evaluate the impact of Pro-Ca on the variety in three training systems were: one-year-shoot length, internode length, dormant pruning weights, number of flower clusters per tree, photosynthetic carbon assimilation rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, chlorophyll determination (by SPAD and chemical extraction), leaf mineral analysis (macro and micro-nutrients), yield per tree, fruit size distribution and packout. The present results confirmed the effectiveness of the Pro-Ca in reducing the canopy growth and vigor in ‘WA 38′, with diminished internode length, total shoot length, and lower amount of pruned material. Leaf gas exchange parameters and chlorophyll quantification highlighted an alteration of tree physiology by Pro-Ca application with increased transpiration, stomatal conductance, intercellular CO2 concentration, and higher concentrations of chlorophyll a and b with respect to untreated trees. Pro-Ca-treated- ‘WA 38′ trees did not show any negative effect on productivity; rather, an increased average fruit mass and an enhanced proportion of apples in the extra-large size category compared to control. Fewer significant differences were found in the comparison between the training systems. Overall, the 3-axis system showed a higher yield and greater number of flower clusters per tree with a lower average area of each leader in comparison to 1-axis. Further investigations will shed light on ‘WA 38′ tree performance, productivity, and fruit quality after multiple years of Pro-Ca treatment to offer orchard management recommendations for a modern, top-worked, machine-friendly orchard.