Problem based learning, in which events from daily life are presented as interesting scenarios, is one of the active learning approaches that encourages students to self-direct learning. Problem based learning, generally used in higher education, requires students to use high end thinking skills in learning environments. In order to use effectively for secondary students, concept cartoons can be integrated to problem based learning environment. Concept cartoons provide alternative views and help students at problem solving stage. So, in this study the effects of concept cartoons and problem based learning on students' inquiry learning skill perceptions and levels of relating knowledge with daily life were examined. Two experiment groups and one control group were formed and pre test-post test control group quasi experimental design was used in this research. During four weeks experimental practice, courses were continued with concept cartoon integrated problem based learning in experiment group 1 while only problem based learning was used in experiment group 2 and science program activities was used in control group. 553 sixth grade students (13-14 age group) from 9 different middle schools in Turkey participated in this study. Inquiry learning skills perception scale and knowledge-daily life relating open ended questions were used as data collection tools. In the result of the data analysis, it was found that students' inquiry learning skill perceptions scores differ significantly in favor of experiment groups. However, no significant difference found between groups in terms of knowledge-daily life relation scores.