The coursework was structured in 5 main courses at the S. Anna School in Pisa:

• Mathematics for Social Sciences
• Statistics and Econometrics
• Microeconomics
• Macroeconomics
• History of Economic Thought and Economic History.

Each course was organized into modules. The current list of compulsory first-year modules was:
1. Mathematics for Social Sciences

• Linear Algebra
• Calculus
• Differential Equations
• Static Optimization
• Dynamic Optimization
• Introduction to Stochastic Processes

2. Statistics and Econometrics

• Basics of Statistics and Econometrics
• Time Series
• Microeconometrics

3. Microeconomics

• Consumption Production
• Markets and Intro to Equilibrium
• Topics in General Equilibrium
• Game Theory
• Decision Theory
• Industrial Organization
• Organizational Economics
• Information, Knowledge and Innovation
• Technical Change and Industrial Dynamics

4. Macroeconomics

• Stylized Facts
• Introduction to Macroeconomics
• Economic Growth: Theory and Empirics
• Dynamic Macroeconomics I and II
• Topics in Macro: Consumption and Investment
• Evolutionary Macroeconomics
• History of Economic Thought and Economic History
• Economic History
• History of Economic Thought.

At the beginning of the second year of the program, short intensive modules in a few ed areas were offered in order to introduce the students to the international state-of-the-art of research. Modules might include:

• Innovation and industrial dynamics (Advanced);
• Neuroeconomics and cognitive foundations of economic and social behavior;
• Philosophical foundations and implications of economic theory and other social sciences;
• Economic and human development and welfare;
• Analysis and management of extreme risks;
• Law and Economics.

Student had access to one module available at the S. Anna School in Pisa., which included: Agent-based Computational Economics, International Trade, Labor Economics, Evolutionary models of innovation, growth and growth fluctuations.