The article presents the results of the application of an original methodology for designing residential buildings with a positive energy balance in accordance with the principles of sustainable development. The methodology was verified using a computational example involving the selection of a compromise solution for a single-family residential building with a positive energy balance located in Warsaw, Poland. Three different models of decision-makers’ preferences were created, taking into account selected decision sub-criteria. Three technical solutions were identified, permissible according to the principles and guidelines for designing buildings with a positive energy balance. As a result of the performed calculations, the final order of the analyzed variants was obtained, from the most preferred to the least accepted solution. Variant 2 is definitely the most advantageous solution, being the best in a group of 20 to 26 evaluation sub-criteria—depending on the adopted model of the decision-maker’s preferences. Its ranking index Ri ranged from 0.773 to 0.764, while for the other variants it was much lower and varied from 0.258 to 0.268 for variant 1, and from 0.208 to 0.226 for variant 3. The methodology used for the case study proved to be applicable. The developed methodology facilitates the process of designing residential buildings with a positive energy balance, which is an extremely complex process.