理学硕士（MS）计划旨在为计划在完成MS计划后直接从事职业而不是继续攻读博士学位课程的学生。MS计划也适合有兴趣从事研究项目但不确定是否要对博士学位计划做出多年承诺的学生。该计划的目的是扩大学生的学习范围。他的知识深度大大超出了计算机科学或相关领域的BA / BS。耶鲁计算机科学硕士为学生提供了与老师进行一对一的小班学习的独特机会，一旦被录取，学生可以选择遵循通用课程，也可以申请生物信息学专业课程之一或在计算机和艺术。研究生课程主任（DGS）为普通课程的学生提供建议。田径学院会向专业田径课程的学生提供建议
To qualify for the Master of Science degree, a student must pass eight courses at the 500-level or above in the Computer Science Department. Advanced graduate courses in other departments that involve concepts from computer science and are particularly relevant to an individual program may, with permission of the Director of Graduate Studies, be counted towards the degree. Generally at most two such courses may be used to satisfy the requirements of the Master's Program. Here an advanced course is generally one with at least one intermediate course as a prerequisite and an intermediate course is generally one with at least one (introductory) course as a prerequisite. But five courses must be in Computer Science.