A system and method for reconciling a healthcare payment account includes receiving: (a) a first file that includes sorted and rebalanced explanation of benefits information from a healthcare payer, the first file generated by segregating comingled data for multiple healthcare providers or accounting systems; (b) a second file that includes payment information for a bank account of a healthcare provider; and, (c) a third file that includes accounting information from the healthcare provider; using reassociation and file splitting processes to match transactions of at least two files using rules based logic, and to calculate variances of transactions between at least two files; and, displaying at least one of variance via at least one GUI to facilitate reconciliation.