Category judging takes place on Friday from 7:00 – 9:30 p.m. Each category is assigned a group of judges with a captain. Each project is judged by a minimum of 3 judges. At the end of the evening, projects are placed (1^st, 2^nd, or 3^rd ) and honorable mentions are awarded. The judging follows a common standard for all categories based on the ISEF judging guidelines. Projects are not placed based on the quality within a specific category. As a result, a category may include two projects that can receive the same placement (i.e. two projects can be awarded first place). Similarly, it is not necessary that every category will award a first, second and third place. For example at the discretion of the judging committee, no first place may be awarded based on the quality of projects in that category. Category judges also provide written feedback on strengths and areas of improvement for each project.

Special awards judging takes place on Saturday from 9:00 a.m. till noon. The types of special awards vary from being specific science areas, like the Ceramic Society Award, to more general awards such as the Homebuilt Apparatus Award. Hence, projects may be visited by varying number of judges depending on their eligibility for the different awards.

On Saturday morning, the ISEF panel comprising captains from the individual categories determines the finalists for the ISEF trip awards. A maximum of fifteen finalists are selected from the first and second place category winners. At least five finalists are selected from the junior division. All finalists give a ten minute presentation to the judging panel at the ISEF symposium, which is held Saturday afternoon from 1:00 to 4:00 p.m. Following the ISEF panel presentations, four winners are chosen for the trip awards, two from the junior division and two from the senior division.