After joining the European Union the Czech Republic should respond positively to the challenges of the Lisbon Strategy, and start to build prerequisites for a knowledge-based economy. It should actively participate in building the new knowledge society in Europe as envisaged by the Lisbon European Council in 2000 in the Lisbon Strategy. The paper brings about the arguments that the Czech Republic should deliberately undergo the second transformation leading to the knowledge-based economy. To underpin the arguments selected structural data describing characteristics of education, science and research and development in Finland and the Czech Republic are used. In conclusions needed reforms and the policy changes are briefly discussed.