The student, Wei Zexi, 21, died last month of a rare form of cancer and China's Internet regulator said on Monday it would investigate Baidu over the case.
Wei had searched Baidu for the best place for treatment, finding a department under the Second Hospital of Beijing Armed Police Corps which offered an experimental treatment that ultimately failed, state media reported this week.
The health ministry, along with military health departments, would jointly investigate the hospital, the National Health and Family Planning Commission said in a short statement on its website.
The ministry did not give further details about the investigation but said the case had drawn widespread public attention.
Before dying, Wei accused Baidu online of promoting false medical information, and the hospital for misleading advertising in claiming a high success rate for the treatment, state radio said.
Baidu said in a statement it deeply regretted Wei's death, and it would fully cooperate with the investigation.
Reuters was not able to reach the hospital for comment.
Baidu's shares dropped sharply after the investigation was announced on fears it may hit its advertising revenues and that it could face a sharp response from regulators who are keenly sensitive to healthcare-related scandals.
In a separate statement, the ministry said an inter-agency team would be set up to crack down on hospital ticket "scalpers" and online healthcare touts, a grey market of buying and selling access to healthcare which has drawn public anger.
The healthcare system is plagued by touts trading appointment tickets outside hospitals and a murky world online of healthcare advertisements offering cheap medicine or access to unapproved or experimental procedures.
Reuters reported in April ticket touts were defying a crackdown launched at the beginning of the year, casting light on the scale of the challenge China faces as it looks to overhaul a creaking, under-funded public health system.
The ministry said it would speed up reforms, improve regulatory systems and standardize how operators published information to "get rid of the soil in which ticket scalpers and online touts survive".