Real-world classification data usually contain noise, which can affect the accuracy of the models and their complexity. In this context, an interesting approach to reduce the effects of noise is building ensembles of classifiers, which traditionally have been credited with the ability to tackle difficult problems. Among the alternatives to build ensembles with noisy data, bagging has shown some potential in the specialized literature. However, existing works in this field are limited and only focus on the study of noise based on a random mislabeling, which is unlikely to occur in real-world applications. Recent research shows that other types of noise, such as that occurring at class boundaries, are more common and challenging for classification algorithms. This paper delves into the analysis of the usage of bagging techniques in these complex problems, in which noise affects the decision boundaries among classes. In order to investigate whether bagging is able to reduce the impact of borderline noise, an experimental study is carried out considering a large number of datasets with different noise levels, and several noise models and classification algorithms. The results obtained reflect that bagging obtains a better accuracy and robustness than the individual models with this complex type of noise. The highest improvements in average accuracy are around 2–4% and are generally found at medium-high noise levels (from 15–20% onwards). The partial consideration of noisy samples when creating the subsamples from the original training set in bagging can make it so that only some parts of the decision boundaries among classes are impaired when building each model, reducing the impact of noise in the global system.