Sri Lanka has experienced a massive demographic, environmental, economic and social transition in recent decades. Over this period of time the country has undergone rapid urbanization leading to accompanying shifts in lifestyle and it suffers a double burden of under- and over-nutrition. Current programmes in the country focus on improving the dietary behaviour of secondary school students. The purpose of this study was to investigate principal's perceptions on barriers to healthy dietary choice among pupils within a socio-ecological framework. Focus groups (n = 11) were carried out with school principals and staff (n = 55) in two rural districts of Sri Lanka. Principals identified a number of barriers to healthy dietary choice by students, which could be found at a number of levels of influence of a socio-ecological framework: (i) structural level barriers included educational and agricultural policies, (ii) living and working level barriers included employment opportunities and local food production, (iii) social and community level barriers included traditions and social/cultural beliefs and (iv) individual level barriers included knowledge and preference. Findings from this study suggest that the barriers to healthy dietary choice amongst secondary school students in Sri Lanka occur at many levels supporting the use of multifactorial programmes to promote healthy eating. Only from understanding these barriers and finding ways to counter them can we hope to reduce the double burden of under- and over-nutrition the country is currently suffering.