Expert geoscientists think in terms of systems that involve multiple processes with complex interactions. Earth system science has become increasingly important at the professional level, and an understanding of systems is a key learning goal at all levels of the earth science curriculum. In this paper, research in the cognitive and learning sciences is brought to bear on the question of how students learn systems thinking and on the challenges of developing effective instructional programs. The research suggests that learning systems concepts is difficult and that it involves extended learning progressions, requiring structured curricular integration across levels of K–16 instruction. Following a discussion of these challenges, current instructional innovations are outlined, and an agenda for needed research on learning and teaching systems thinking is proposed.