With the accession of the Republic of Croatia to the European Union and the opening of the European Structural and Investment Funds, secondary schools were given new opportunities for improvement, but also have faced new challenges in successful project applications. Involving schools in writing and implementing the European Union funded projects presents a major challenge and brings many changes. The role of the headmaster in implementing changes is crucial. To implement changes successfully, the headmasters direct employees towards completion of mutual vision, motivate them to participate in school development, as well as in the projects. One of the most desirable models of leadership related to change implementations and mutual actions of the headmasters and employees, is the transformational leadership style. The purpose of this paper is to examine secondary schools’ effectiveness in applying projects to European structural and investment funds and to examine if there is a connection between the transformational leadership style of the headmasters and the success of secondary schools in applying the projects to the EU funds. Analysis of the published financing decisions has shown that Varaždin county schools have been the most successful in applying the projects to European Structural and Investment funds, both in number and value of the projects. Therefore, an empirical research has been undertaken in Varaždin County, by interviewing secondary school headmasters, aiming to find the key qualities of leadership in schools successful in applying projects to the EU funds. Assessment of the leadership style using the Multifactor leadership questionnaire, tested the presence of transformational leadership style and examined the connection of this style with the success in applying to the aforementioned funds. This empirical research proved that the secondary school headmasters in Varaždin county who have been the most successful in applying projects to the EU funds share a high level of transformational leadership style, and that there is a connection between the transformational leadership style of secondary school headmasters and the schools’ success in applying projects to the EU funds, which proved the first hypothesis H.1 as true. The second and third hypothesis, which assumed that transformational leadership style of headmasters is more related to higher number and higher value of the approved projects than transactional leadership style, have not been confirmed by this research.