Featured Application This paper and its findings are important for any clinic that is thinking about setting up a navigation system for its ENT department, concerning the costs, efficiency in the operating room, and applicability for training purposes. (1) Background: The use of navigation systems is rarely necessary for routine sinus surgery. They may prove to be advantageous for difficult operations, for example, in finding structures that are difficult to reach, in the treatment of cancers, or in revisional surgery. Navigation systems are also said to have positive effects on the self-confidence of surgeons in stressful situations and in the training of doctors. (2) Methods: This retrospective study included patients who underwent surgical treatment for chronic sinusitis from 2012 to 2016 at the ENT clinic of the University Hospital, Erlangen. Two groups were formed; one includes patients without navigated sinus surgery, the other includes those with navigation. The incision-suture times of both groups and cost analysis are compared. An appropriate cost estimate for sinus surgery is determined. (3) Results: From the available results, no economically efficient navigation systems in sinus surgery at the ENT clinic can be shown. The main reason is that lengthening the operating time leads to higher costs. (4) Conclusions: Although the use of a navigation system for endonasal sinus surgery cannot be economically justified, it is an important tool, especially in cases with complex anatomical conditions, and the system is essential for training purposes.