Extensible Markup Language (XML) is used to exchange messages across different networks due to its flexibility and adaptability. Due to the wide usage of XML documents over internet there arises a need to protect these documents to provide data confidentiality and privacy. There are various cryptographic algorithms proposed to encrypt XML documents to address the issue of security. In this paper we are proposing a new public key cryptographic algorithm called XML Batch Multi-Prime RSA (XBMRSA) to encrypt sections of XML document based on Multi-Prime RSA technique. A detailed comparative study of standard RSA and XBMRSA is carried out by considering parameters like time required to encrypt and decrypt the XML file and size of the encrypted file. XBMRSA has provided better results as it takes less time to encrypt and decrypt the XML data.