While conventional interventions and evaluations address the symptoms of the learning crisis, there is growing acknowledgement that widespread and sustained learning improvements will require systems approaches that diagnose and address the root causes of low learning. This paper presents and applies three methods to evaluate education systems and inform how to improve system coherence for learning. First, we use learning trajectories to evaluate the dynamics of children’s learning in 22 low- and middle-income countries. Second, we present a set of principles called the ALIGNS principles and show how they can be used to evaluate and improve alignment of curricula, assessments, and teacher support and instruction. Finally, we present a systems diagnostic framework and apply it to a program in South Africa, showing how the program takes a systems approach to improve learning. These tools help concretize systems thinking and bring insights to bear on the design and evaluation of policies and programs intended to improve learning.