The first level of the Student Center houses the Marketplace where refreshments and snacks can be enjoyed and College branded logo items are available for purchase. In addition, student resident mailboxes and Student Government Association office, as well as the BLS classroom are located on the floor. On the second level is Howard Hall, a multi-purpose room that provides open space for large gatherings and events. The second level also home to the Clarkson College Testing Center.

In the Main Building at 42 and Dodge Streets, the lower level (LL) houses a full energized laboratory and classroom for the Radiography and Medical Imaging programs as well as an additional science lab.

On the first floor lobby of Main Building is the hub for the College. The Enrollment Department, Academic Advisors, Registrar, Financial Aid, Student Accounts, and Professional Development are housed in this suite. This location provides centralization of student services and information to students and visitors.  Professional Development provides nurse aide, life support and non-credit classes for the community. 

The second floor of the Main Building houses the Library and Academic Support Services. Including the Clarkson Service League Library and Student Success Center. Maintaining the convenient hours of 24-7, the Library provides students with knowledgeable staff and resources necessary to complete projects and conduct research. Room 203 is the J.W. Upright Success Center, which caters to the study, tutoring and counseling needs of students.

The second floor of the Main Building also houses classrooms and a science lab for the anatomy, physiology, chemistry and biology classes. Just beyond the science lab is second floor south, a mini Marketplace and the skills laboratory and classroom for the Physical Therapist Assistant program.

The third floor of the Main Building provides the College with one large classroom and houses the Information Technology department. The third floor also includes a brand new Clarkson College Interactive Learning Center (ILC) offering a multitaction wall and anatomage tables for interactive learning.

The fourth floor of the Main Building houses the Interprofessional Learning Center, which includes three simulation labs, including an operating room, two classrooms, four patient rooms and a community health space. The fourth floor also houses a Nurse Aide instructor office. 

Clarkson College faculty offices, director of Undergraduate Nursing, assistant directors of Undergraduate Nursing, director of Radiography and Medical Imaging and assistant director of Radiography and Medical Imaging are located on the fifth floor of the Main Building.

The sixth floor of the Main Building houses the administrative offices of the president, vice president of Academic Affairs, vice president of Operations and Student Affairs, director of Graduate Nursing, director of Community Health and Interprofessional Education, director of Doctor in Healthcare Education & Leadership, director of Healthcare Business, director of General Education, Fiscal Services, Facilities, director of Professional Development, Director of Resesarch and Compliance, Human Resources, Strategic Communications and Alumni Relations.

The Clarkson Commons and Education Center is connected to the main buidling through a newly renovated skywalk. The first floor houses a reception area, faculty offices, and two conference rooms. The second floor houses has three private study rooms, two large classrooms and a classroom and study room dedicated to the Nurse Anesthesia program. The Center for Teaching Excellence (CTE) is housed on the second floor and supports teaching and learning at Clarkson College by assisting faculty and academic programs in their continued pursuit of course improvement and student learning. CTE manages and coordinates instructional design, faculty development, online education, diversity and institutional effectiveness services for faculty and academic program needs. The Academic Travel Abroad (ATA) program is housed on the second floor as well. A student lactation room is available on the second floor and accessible at all times.