应用物理研究生在其研究兴趣领域中，在教职员工的指导和建议下发展自己的学习和研究课程。这些课程通常从应用物理学，工程与应用科学学院和物理系的列表中选择，领域包括理论和实验凝聚态和材料物理学，光学和激光物理学，量子工程和纳米科学等领域。具体计划包括表面和界面科学，第一性原理电子结构方法，光子材料和器件，复合氧化物，磁和超导人工工程系统，量子计算和超导器件研究，量子传输和纳米管物理学，量子光学和随机激光器。
A Ph.D. in Applied Physics at Yale is designed to certify two distinct educational attainments: mastery of the subject matter and demonstrated ability to make original research contributions to the field, in addition to training as a professional in the field of applied physics. Graduate students pursuing this degree are required to follow the guidelines in this document as well as all of the rules and procedures of the Graduate School of Arts and Sciences and of the University. Some of those rules and procedures are included in this document, and others are in the Policies and Regulations in the Bulletin of the Graduate School of Arts and Sciences. The department recognizes that a graduate student may face extraordinary circumstances during their time at Yale that impede their progress. When facing such circumstances, students are encouraged to communicate with their advisor, the DGS, the Department Chair, and staff at the Graduate School or elsewhere within the university. All of these people are available to help graduate students at Yale reach their highest potential within the degree program. Throughout their graduate career, the student is always expected to be in good standing, as described in detail below.