Faculty of Science, originated with the beginning of the founding of the university in 1994, was combined with the Faculty of Information Technology, until it was separated in 2015, in response to the urgent need for society for qualified graduates in the disciplines of basic sciences. The faculty currently made up of three academic departments, namely: mathematics, physics, and the unity of service courses, all of which basically use English for teaching. The faculty is currently considering introducing two departments: chemistry and biology. The university provides the faculty with elite academic staff members and administrators. Faculty of Science represents the basic structure for the various disciplines in Zarqa University.

The faculty offers a bachelor's degree in mathematics and physics disciplines after finishing study (132 credit hours) with a cumulative average over (60%). The college also offers graduate programs, the Master's program in mathematics.

Department of Mathematics: The department was established and gains specialized accreditation since the founding of the university in 1994. Mathematics is the major science among all natural sciences in addition to the importance of this science in human lives and communities. The university has prepared an integrated a plan to the department includes: Modern Algebra, real and complex analysis, topology, statistics, differential equations and Operations Research, and others.

Department of Physics: The department of physics was established since the university was founded, under the name of medical physics and was providing basic materials in physics for many departments and faculties. In 2011 it gained specialized accreditation under the name of the Department of Physics. The university established for this purposes all specialized laboratories such as physics laboratory 1 and 2 and the advance physics laboratory 1 and 2, Laboratory of Electronics and Optics Laboratory. The department offers basic and advanced materials/courses in the physical sciences, such as electronics and optics science and modern physics, classical mechanics, thermal and nuclear physics, and others.

Unit of service courses This unit was established and gained specialized accreditation in 2015, since then it provides the basic material/courses for mathematics department and many faculties such as information technology, engineering, pharmacy, nursing, faculty of allied medical sciences.

• The faculty organizes an international refereed and periodically conference in mathematics and statistics once every two years, which has been held four times so far.
• The faculty began in 2011/2012 graduate program (master's degree) in mathematics.
• First Conference on Medical Physics, held by the college in 1999/2000.