On August 14, 2000, Jischke became the tenth president of Purdue University, succeeding Steven C. Beering, who stepped down after 17 years as Purdue's president.
From the beginning of his administration, Jischke established the goal of "making a great university into a preeminent university."

To accomplish this goal, Jischke and the Purdue University Board of Trustees developed a strategic plan for the university, proposed sweeping changes, and introduced ambitious fundraising and construction agendas.
The scope of the plan extended beyond the university campus, to the state of Indiana at large.
Jischke and the trustees saw a stronger Purdue leading an economic resurgence for the entire state.

The five-year strategic plan was adopted in November 2001.
The plan called for data-driven decision making, focusing on collecting data on various performance benchmarks for comparison with peer institutions.
Jischke also advocated steps to improve diversity, expand interdisciplinary research, add 300 new faculty positions, and engage government and business leaders to advance economic development.
One of the most visible expressions of his vision is Discovery Park, a $100 million multidisciplinary research and entrepreneurial complex on Purdue's West Lafayette campus.

Jischke also led the way in the "Campaign for Purdue," a $1.5 billion fund-raising operation, launched in September 2002 in support of the strategic plan.
The campaign designated $200 million for student scholarships and fellowships, $200 million to attract and retain a quality faculty, $200 million for programs and centers, $600 million for facilities and equipment and $100 million in unrestricted funds.
The plan was the largest such fundraising campaign in the history of higher education in Indiana.
Jischke also focused on building alumni support and creating educational partnerships within the state.

In October 2004, Jischke testified before the United States Senate Committee on Foreign Relations on the value of international students, their decline in U.S. university enrollment since the September 11 attacks, and recommendations for visa policy reform.

On August 4, 2006, Jischke announced he would be stepping down from the president's post at the end of the 2006–07 fiscal year.
 He stated he would be taking a year off from public life at that time.

On May 7, 2007, the Purdue University Board of Trustees announced the appointment of France A. Córdova to succeed Jischke as the university's 11th president effective July 16, 2007.

On May 12, 2007, Jischke was awarded an honorary doctorate degree from Purdue University's College of Engineering.
In June 2007, Jischke was awarded the university's first Neil Armstrong Medal of Excellence by Armstrong himself, along with the Sagamore of the Wabash, the highest honor from the governor of Indiana.
On August 14, 2000, Jischke became the tenth president of Purdue University, succeeding Steven C. Beering, who stepped down after 17 years as Purdue's president. From the beginning of his administration, Jischke established the goal of "making a great university into a preeminent university."
To accomplish this goal, Jischke and the Purdue University Board of Trustees developed a strategic plan for the university, proposed sweeping changes, and introduced ambitious fundraising and construction agendas. The scope of the plan extended beyond the university campus, to the state of Indiana at large. Jischke and the trustees saw a stronger Purdue leading an economic resurgence for the entire state.
The five-year strategic plan was adopted in November 2001. The plan called for data-driven decision making, focusing on collecting data on various performance benchmarks for comparison with peer institutions. Jischke also advocated steps to improve diversity, expand interdisciplinary research, add 300 new faculty positions, and engage government and business leaders to advance economic development. One of the most visible expressions of his vision is Discovery Park, a $100 million multidisciplinary research and entrepreneurial complex on Purdue's West Lafayette campus.
Jischke also led the way in the "Campaign for Purdue," a $1.5 billion fund-raising operation, launched in September 2002 in support of the strategic plan. The campaign designated $200 million for student scholarships and fellowships, $200 million to attract and retain a quality faculty, $200 million for programs and centers, $600 million for facilities and equipment and $100 million in unrestricted funds. The plan was the largest such fundraising campaign in the history of higher education in Indiana. Jischke also focused on building alumni support and creating educational partnerships within the state.
In October 2004, Jischke testified before the United States Senate Committee on Foreign Relations on the value of international students, their decline in U.S. university enrollment since the September 11 attacks, and recommendations for visa policy reform.
On August 4, 2006, Jischke announced he would be stepping down from the president's post at the end of the 2006–07 fiscal year.  He stated he would be taking a year off from public life at that time.
On May 7, 2007, the Purdue University Board of Trustees announced the appointment of France A. Córdova to succeed Jischke as the university's 11th president effective July 16, 2007.
On May 12, 2007, Jischke was awarded an honorary doctorate degree from Purdue University's College of Engineering. In June 2007, Jischke was awarded the university's first Neil Armstrong Medal of Excellence by Armstrong himself, along with the Sagamore of the Wabash, the highest honor from the governor of Indiana.
Martin C. Jischke