计算科学与工程（CSE）是一个快速发展的领域，它利用计算的能力来应对自然和社会科学以及所有工程领域的重大挑战。与哈佛大学对基础知识的重视相一致，CSE学位课程侧重于跨学科的跨领域数学和计算原理。完成课程的学生将掌握各种方法，包括用于复杂系统建模和仿真的数学技术，并行编程和协作软件开发，以及用于组织，探索，可视化，处理和分析非常大的数据集的有效方法。哈佛大学计算科学与工程专业的第二个学位是两年制工程硕士（ME）硕士学位是一个两年制课程，需要论文。预计该学生将在第二年的大部分时间里进行研究。
The Master of Engineering (ME) in CSE is a two-year program requiring students to complete and defend a thesis project. ME students must satisfy the same 8 course requirements as SM students. In addition, they will spend the majority of their second year working on a substantial computational project that culminates in the submission and oral defense of a master's thesis. While all thesis projects must have a significant computational component, students are given leeway in finding a project that applies computation to solve a problem in a domain of study that fits with their background and interest. All ME students must find a research advisor and submit a master's of engineering thesis proposal and a letter of support from the thesis advisor by mid-March of their first year of study. Thesis proposals will be evaluated by the CSE faculty committee and only those students whose proposals are accepted will be allowed to continue for the second year of the program.