For security and privacy, often the user's data are stored on a cloud storage server in an encrypted form. Such data however, are required to be processed in terms of search queries, aggregation, clustering or classification. For better data analysis, the stored data on the server and a result of the processed data should be in lexicographic order. The conventional recourse such as offloading-decryption-ordering, may not be an efficient mechanism for huge data collection since it involves large communication overhead and breach of data privacy. Functional Encryption (FE) provides a viable solution as it offers encrypted data processing at the remote server site while preserving the privacy of the processed data. In this paper, we propose an improvised functional encryption for encrypted data ordering that takes as input multiple ciphertexts and orders them at the server site, without compromising data privacy. As ordering involves at least two data, we formalize an order function using multi-input functional encryption with obfuscation. The proposed approach, Multi-Input Functional Encryption for Ordering (MIFEO) runs an order function on multiple ciphertexts at the server site, arranges them in order and generates an ordered set of ciphertexts. Using online E-health system as a case study, we demonstrate the applicability of the proposed MIFEO scheme in a practical scenario.