Interactive segmentation is commonly used in medical image analysis to obtain precise, pixel-level labeling, typically involving iterative user input to correct mislabeled regions. However, existing approaches often fail to fully utilize user knowledge from interactive inputs and achieve comprehensive feature extraction. Specifically, these methods tend to treat all mislabeled regions equally, selecting them randomly for refinement without evaluating each region's potential impact on segmentation quality. Additionally, most models rely solely on spatial domain features, overlooking frequency domain information that could enhance feature extraction and improve performance. To address these limitations, we propose ActiveFreq, a novel interactive segmentation framework that integrates active learning and frequency domain analysis to minimize human intervention while achieving high-quality labeling. ActiveFreq introduces AcSelect, an autonomous module that prioritizes the most informative mislabeled regions, ensuring maximum performance gain from each click. Moreover, we develop FreqFormer, a segmentation backbone incorporating a Fourier transform module to map features from the spatial to the frequency domain, enabling richer feature extraction. Evaluations on the ISIC-2017 and OAI-ZIB datasets demonstrate that ActiveFreq achieves high performance with reduced user interaction, achieving 3.74 NoC@90 on ISIC-2017 and 9.27 NoC@90 on OAI-ZIB, with 23.5% and 12.8% improvements over previous best results, respectively. Under minimal input conditions, such as two clicks, ActiveFreq reaches mIoU scores of 85.29% and 75.76% on ISIC-2017 and OAI-ZIB, highlighting its efficiency and accuracy in interactive medical segmentation.