In the Surveillance Tool for Outcome-based Comparison of FREEdom from infection (STOC free) project (https://www.stocfree.eu), a data collection tool was constructed to facilitate standardised collection of input data, and a model was developed to allow a standardised and harmonised comparison of different control programmes’ (CP) output for cattle diseases. The STOC free model can be used to evaluate the probability of freedom from infection for herds in CPs and to determine whether they comply with pre-defined output-based standards of the European Union. Bovine viral diarrhoea virus (BVDV) was chosen as the case disease for this project because of the diversity in CPs in the six participating countries. Detailed BVDV CP and risk factor information was collected using a data collection tool. For inclusion of the data in the STOC free model, key aspects and default values were quantified. A Bayesian hidden Markov model was deemed appropriate, and a model was developed for BVDV CPs. The model was tested and validated using real BVDV CP data from partner countries and corresponding computer code was made publicly available. The STOC free model focuses on herd level data, noting that animal level data can be included after aggregation to herd level. The STOC free model is applicable to diseases that are endemic, given that the model needs the presence of some infection to estimate its parameters and enable convergence. In countries where infection free status has been achieved, a scenario tree model could be a better suited tool. Further work is recommended to generalise the STOC free model to other diseases.