Haim Harari became head of the Department of Science Teaching at the Weizmann Institute at age 29 and Dean of the Feinberg Graduate School of the Weizmann Institute, in 1972, at age 31, serving till 1978.
In 1976 he was appointed a member of the Council of Higher Education, the supreme body in charge of accreditation of Institutions of Higher Education in Israel. In 1979 he was elected as Chairman of the Planning and Budgeting Committee (PBC) of the Council of Higher Education, serving two terms until 1985. The PBC has the full authority of distributing the entire Israeli Government budget for Higher Education and basic Research to all Academic Institutions in Israel. It also has the authority to approve or prevent the establishment of new Faculties, Schools and Departments in Universities and other Academic Institutions, based on budgetary considerations and national needs.
During his two terms, the PBC initiated numerous activities, which left their mark on Israel’s academic system. Among them: the creation of the first university computer network, second only to the USA; the first forecast of national needs in various academic professions, accompanied by expansion or reduction in size of corresponding professional academic schools; expansion of engineering and computer science schools, laying the foundation many of the achievements of to Israel's high-tech industry; conversion of some Teachers Colleges to Academic Institutions and closing of others; expansion of the Israel National Science Foundation at a time of rapidly diminishing Higher Education budgets; doubling of university tuition accompanied by generous fellowships to students willing to help an underprivileged child through the Perach mentoring project; establishment of a first Veterinary School and a new Dental School; first-time academic programs in topics such as social work, paramedical professions, accounting, visual arts, and music; Establishing the independent or semi-independent status of separate Institute for Desert Research, the Eilat inter-university institute of marine science, and the Israel academic center in Cairo, All of these were achieved at a time when the annual inflation rate was ranging between 100% and 400%, budgets had to be updated on a weekly basis and Government support was continuously slashed.
In 1988 Harari was elected President of the Weizmann Institute, serving in this position for 13 years, leaving office of his own decision in 2001. During his years in office, the Institute entered numerous new scientific fields and projects, built several dozen new buildings, and raised over one Billion Dollars in philanthropic money. The endowment of the Institute quadrupled in these years, exceeding half a billion dollars.
Major investments and recruitments were made in semi-conductor physics, brain imaging, computer science, nano-chemistry, molecular genetics, environmental science, bioinformatics, magnetic resonance studies, optical science, cancer research, structural biology, and other research areas. The royalty stream from sales of products patented by the Weizmann Institute exceeded (in absolute numbers) that of Harvard, Stanford, M.I.T. or Princeton, in spite of the huge mismatch in the relative sizes. This has been achieved without sacrificing the notion that the Weizmann Institute continues to be an Institute of Basic Research.
The Institute has been opened to the Israeli and the international public with the establishment of a Visitor Center, an outdoor Science Museum ("Clore Garden of Science"), a museum in the historic Weizmann house, self-guided tours of campus facilities, festive public science “happenings” on major holidays and numerous science education activities for the general public.
Upon leaving the Presidency of the Weizmann Institute, Harari initiated the creation of two new independent legal entities, both within the world of the Weizmann Institute. In 1999 he founded and became the Chairman of the Board of the newly established Davidson Institute of Science Education, dealing with all aspects of science education for teachers, pre-college school students, and the general public. He is also the founding Chairman of the Management Committee of the newly established Weizmann Global Endowment Management Trust in New York, an organization managing the endowments of the various independent international bodies which are supporting the Weizmann Institute.
In 2006 Harari has been approached by the Austrian scientific community to help create, near Vienna, an entirely new Institute of basic Research, largely modeled along the lines of the Weizmann Institute. He chaired the International Committee that established the blueprint for the new Institute, contributed significantly to the preparation of a law enacted by Parliament, defining the structure of the new Institute, was elected to its first Board of Trustees, appointed Chair of the Executive Committee of the Board and Chair of the Search Committee for the first president and served, from December 2006 till September 2009, as the person holding the responsibility of an acting president, during the creation of the Institute. In September 2009, Professor Tom Henzinger became the first president of the Institute of Science and Technology Austria and Harari remains as chair of the Executive Committee of the Board of Trustees till 2020. According to normalized ranking, IST-Austria was ranked 3rd globally by the Nature Index 2019 for best research quality, next only to the Weizmann Institute, which became the 2nd best research institute worldwide. This normalization enables the comparison between institutions of different sizes, allowing various small institutes, which have a significant research impact, to come into the light.
At different other times, he has been asked to advise organizations and governments, including Brazil and China, planning to establish a variety of new scientific institutions.
In 2021 Harari was the recipient of the "Higher Education Prize" by the Israeli Council for Higher Education "in recognition of a groundbreaking, inspiring academic endeavor that combines scientific excellence and contribution to the community and society".