Globalization of nowadays education and science promoted by various international programmes provides with unique opportunities to renew some old educational approaches connected with linear application of education within higher educational institutions in Lithuania. Nowadays Nature science development confirms fact, that there are more approaches to reality, than finding the only one epistemological truth. In parallel there are several aspects, dimension of the same truth in the complex systems of the reality. Educational process regarding its complexity largely belongs to the complex, nonliner, opened and non-reversal systems. That's why we must be focused on the dynamics of educational components rather than on its components alone, that are at the second rate of importance. Those relations have influence on the whole system change largely. That is the reason why authors employ the theory of Synergy, that` s focused on such kinds of relations. Authors explore the roots of Synergy theory its approaches of application in Educational systems. Project-based learning is kept as one of active forms in the complex education systems. There are emphasized problem solving competences in project-based learning, the synergy of separate cognitive steps in learning process that are reflected in two higher educational institutions within bachelor degree students in Vilniaus kolegija / University of Applied Sciences and master degree students in Vilnius Gediminas Technical University. Peculiarities of Projectbased learning are revealed through review of problem solving application methodology to promote students ` cognitive and meta-cognitive skills, connected to decision making, social, group working skills. Authors emphasize on College level students ` shortages of competences related to finding the right information, structuring of problems components, modelling of project solving strategy. This reveals students paternalistic manner of thinking that impede learning process due to the lack of habits of thinking systemically. That shows shortage of applying innovative educational methods in the College. Respectively, educational experiment revealed, that Master degree students in the University demonstrated much higher achievements in operation of cognitive and meta-cognitive competences in completing problems solving tasks, what demonstrated their success in whole project implementation more, comparing to the Colleges' ones. Authors of this work emphasize the importance of treating all students across the different subjects with problem based learning methodologies in order to improve project implementation skills in Higher educational institutions. (C) 2013 The Authors. Published by Elsevier Ltd.