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A methodology is proposed to aid parameter estimation in fundamental models of pharmaceutical processes. This methodology addresses situations with insufficient data to reliably estimate all parameters, when the estimation is complicated by uncertain independent variables. The proposed method uses an augmented sensitivity matrix to rank the combined set of parameters and uncertain inputs from most estimable to least estimable. An updated mean‐squared‐error criterion is then used to determine the appropriate parameters and inputs that should be estimated, based on the ranked list. A model for one step in a batch pharmaceutical production process with an uncertain initial reactant concentration is used to illustrate the method, revealing that the initial reactant concentration in each batch should be estimated along with three out of six model parameters. Non‐estimable parameters are fixed at their initial values to prevent overfitting. The method will aid error‐in‐variables parameter estimation in many situations involving limited data. [ABSTRACT FROM AUTHOR]