Introduction: The incidence of breast cancer has risen in Chile, along with the complexity of diagnosis. For accurate diagnosis, it is necessary to complement the morphology assessed with hematoxylin and eosin with additional techniques to evaluate specific tumor markers. Evaluating the impact on costs, time, and productivity of automated techniques integrated with digital pathology solutions is crucial. Objectives: To estimate the impact on costs, time, and productivity of incorporating the automation of the HER2 in situ hybridization technique combined with integrative digital pathology (IDP) in breast cancer diagnosis in a Chilean public provider versus a manual technique. Methods: This economic evaluation adopted a health economics multi-method approach. A decision model was developed to represent the current manual fluorescence in situ hybridization (FISH) scenario versus an automated dual in situ hybridization (DISH) plus IDP in breast cancer diagnosis. Business process management (BPM) methodology was applied for capturing working time and latencies, in combination with a time-driven activity-based costing (TDABC) methodology for estimating direct, total, and average cost (2023 USD) for both scenarios for the following vectors: Human resources, supplies, and equipment, sorted by pre-analytical, analytical, and post-analytical phases. Indirect costs (2023 USD) were also retrieved. Both BPM and TDABC served to estimate labor productivity. Results: In the baseline scenario based on manual FISH, the turnaround time (TAT) was estimated at 1259 min, at an average total cost of $265.67, considering direct and indirect costs for all phases. An average of 20.5 FISH reports were submitted per pathologist monthly during the baseline. The automated DISH plus IDP scenario consumed 203 min per biopsy, at an average total cost of $231.08, considering direct and indirect costs for all phases; it also showed an average of 22.8 submitted reports per pathologist monthly. This represents a decrease of 13.02% in average total costs, an 83.86% decrease in TAT, and an average labor productivity increase of 11.29%. Conclusions: The incorporation of automated DISH plus IDP in the pathology department of this public provider has resulted in reductions in the time required to perform the in situ hybridization technique, a decrease in total costs, and increased productivity. Particular attention should be given to adopting new technologies to accelerate processing times and workflow.