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While you can let the employee know that confidentiality will be kept to the extent possible, you cannot promise complete confidentiality. As part of an employer's legal obligation to investigate and remedy harassment, certain aspects of the investigation may be disclosed to those with a need to know.
The alleged harasser needs to be treated fairly during the investigation and should be given enough information about the complaint to respond effectively. Almost always this includes disclosing the complainant's identity. Reassure the complaining employee that they are protected from retaliation by company policy and the law, and inform the alleged harasser that they cannot retaliate against the complainant or anyone else involved in the investigations.
You can find more information in the Harassment Investigations section of the HR Library.