Here is the following list of some top Colleges offering Masters Degree in Innovation and Entrepreneurship with the name of program

Babson College
Master of Science in Management in Entrepreneurial Leadership

MIT Sloan School of Management
MBA Entrepreneurship & Innovation Track (E&I)

ESADE Business School
MSc in Innovation and Entrepreneurship

Université Catholique de Louvain - UCL Entrepreneurship
Formation interdisciplinaire en création d’entreprise

Rotterdam School of Management
Msc in Strategic Entrepreneurship
MscSocSc (Msc in Social Science) Organizational Innovation and Entrepreneurship

University of Pennsylvania - Wharton School
MBA Entrepreneurial Management

University of Cambridge - Judge Business School
Postgraduate Diploma in Entrepreneurship

ESCP Europe Business School
MS Innover et Entreprendre / MS Innovation and Entrepreneurship

SDA Bocconi School of Management
Master in Imprenditorialità e Strategia Aziendale

Cornell University
MBA Entrepreneurship and Innovation EI Concentration with the Entrepreneurship and Innovation Institute (EII)

Nova School of Business and Economics - Universidade Nova de Lisboa
Innovation and Entrepreneurship

ESSEC Business School
MS Centrale - ESSEC Entrepreneurs

Grenoble Ecole de Management
MS Entrepreneurs - Pédagogie HEC Entrepreneurs

Manchester Business School - Faculty of Humanities
MSc in Innovation Management and Entrepreneurship

Aalto University - School of Business
Entrepreneurship

Northwestern University - Kellogg School of Management
Innovation & Entrepreneurship Major - Levy Entrepreneurial Institute

The University of Sydney
Master of Commerce: Strategy, Innovation and Entrepreneurship

University of Western Ontario - Richard Ivey School of Business
MBA & Certificate in Entrepreneurship with the Pierre Morrissette Institute for Entrepreneurship

University of Texas at Austin Mccombs School of Business
MSc in Technology Commercialization

EMLYON Business School
MS Entreprendre

University of Virginia - Darden School of Business
MBA Entrepreneurship, Innovation and Strategy

Maastricht University
MSc International Business - Entrepreneurship and SME Management

Purdue University - Krannert School of Management
MBA in Technology Innovation & Entrepreneurship

Recanati School of Business, Tel Aviv University
MBA in Management of Technology, Entrepreneurship and Innovation

Nagoya University of Commerce & Business (NUCB)
Business Innovation Program

SKEMA Business School
MSc Entrepreneurship & Innovation

HEC Paris
MS Entrepreneurs

Antwerp Management School
Master of Innovation and Entrepreneurship

University of Limerick - Kemmy Business School
Masters in International Entrepreneurship Management

Católica Lisbon School of Business & Economics - Universidade Catolica Portuguesa
International MSc in Business Administration/Strategy & Entrepreneurship

University of Otago - Otago Business School - Center for Entrepreneurship
Master of Entrepreneurship

University of Florida
Thomas S. Johnson Entrepreneurship Master's Program

University of Texas at Dallas
Innovation and Entrepreneurship

Université Paris-Dauphine
Master Entrepreneuriat et Projets Innovants

University of Groningen - Faculty of Economics and Business
Business Administration - Small Business and Entrepreneurship

York University - Schulich School of Business
MBA Entrepreneurial Studies

University of Glasgow
International Business & Entrepreneurship

The University of Nottingham
MBA Entrepreneurship

Kyoto University - Graduate School of Management
Business Creation and Revitalization Program - Center for Research in Business Administration

Indiana University - Kelley School of Business
Master of Business Administration in Entrepreneurship & Corporate Innovation

SGH - Warsaw School of Economics
The Master Double Degree Program (Technische Universitat Berlin)

EBS Universität Für Wirtschaft Und Recht
Master in Business Innovation

University of Pretoria - Gordon Institute of Business Science
MBA - Entrepreneurship

WHU Vallendar - Otto Beisheim School of Management
MBA specialisation in Entrepreneurship

LUSEM - Lund University School of Economics & Management
Master programme in Entrepreneurship - New Venture Creation

Riga Technical University - Faculty of Engineering Economics and Management (FEEM)
Innovations and Entrepreneurship

Faculty of Economics University of Ljubljana
Master in Entrepreneurship

University of Washington
Leadership MBA Bothell Campus

University of Maryland
MBA Entrepreneurship major / The Dingman Center for Entrepreneurship at the Robert H. Smith School of Business