There are three different programs offered at the University of Tokyo for undergraduate students.
The first two that I will introduce are English programs, and the third one is in Japanese.

PEAK Program Logo
Source: https://peak.c.u-tokyo.ac.jp/whypeak/index.html

(1) PEAK Program
An abbreviation for Programs in English at Komaba, as the name suggests, this program is offered entirely in English. Students who have studied in languages other than Japanese during secondary school are eligible and no knowledge of Japanese is required. PEAK students will study liberal arts for their first two years, and then specialize in either “Japan in East Asia” or “Environmental sciences”.

The University of Tokyo School of Science Logo
Source: https://www.s.u-tokyo.ac.jp/en/logo/

(2) GSC Transfer Program
The lessons offered in this program are in English and have many benefits. For example, according to the University of Tokyo’s website, there is a scholarship offered in which students will receive a monthly stipend of ¥150,000 for up to two years, and students will receive support academically plus have accommodations arranged for them.
Only those who have completed basic Chemistry, Mathematics, Biology, and Physics related subjects in their first and second year of undergraduate studies at their university are eligible.  Prospective students must have undergone secondary and post-secondary education outside of Japan as well.

(3) Japanese Program
This is the same program as the Japanese students. Students who are under government scholarships such as the MEXT Scholarship or apply as a returnee (帰国子女) will study under this program. Depending on your choice of major and choice of foreign language, you will be put into a certain category and class. For example, those who wish to major in Medicine will be put into the category “Science 3”, and those who wish to major in linguistics will be put into the category “Arts 3” and so on. The first two years follow a liberal arts system, and students will specialize in their major from their third year onwards.

The PEAK program is offered at the Komaba Campus, while the GSC Transfer Program is offered at the School of Science, which is in the Hongo Campus. Those who take the Japanese program will have to move to the Hongo Campus in their third year.