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Abstract Significance Resting-state functional connectivity (RSFC) is an important measure in advancing our understanding of brain function and development as well as various neurological and mental disorders. Studying RSFC with functional near-infrared spectroscopy (fNIRS) offers several advantages over functional magnetic resonance imaging (fMRI), especially for clinical and pediatric populations. However, the optimal strategy to estimate RSFC based on fNIRS, particularly in identifying reliable connectivity patterns across chromophores, remains unclear. Establishing robust analysis approaches is essential for reliable and clinically meaningful applications. Aim This study systematically evaluated commonly used analysis methods regarding their effectiveness to detect RSFC patterns within the motor network using both oxygenated (HbO) and deoxygenated (HbR) hemoglobin signals. Approach Near whole-head resting-state fNIRS data were analyzed from 38 participants. RSFC was estimated with five analytical approaches: three seed-based methods (SBA-GLM, SBA-GLM with respiratory regression, and SBA-correlation) and two independent component analyses (ICA) approaches using two different contrast functions. Performance was assessed via receiver operating characteristic analyses based on both anatomical and functional definitions of motor-related connectivity. Areas under the curves (AUC) were statistically compared with DeLong’s test, and the spatial similarity between HbO and HbR RSFC was quantified by correlating RSFC patterns from the two chromophores. Results Across reference definitions and chromophores, ICA consistently achieved higher performance (AUC = 0.82–0.96) in detecting motor-related RSFC than SBA (AUC = 0.63–0.86). Significant differences emerged when functionally defined connectivity references were used, with ICA outperforming SBA across chromophores. Under certain condition, correlational-SBA (AUC = 0.66–0.86) significantly outperformed GLM-based methods (AUC = 0.63–0.85). Finally, ICA results demonstrated greater spatial similarity between obtained HbO and HbR RSFC patterns ( r = 0.90–0.92) than SBA ( r = 0.84–0.86), indicating higher cross-chromophore consistency. Conclusions ICA provides a robust and consistent framework for estimating fNIRS-based RSFC across both HbO and HbR, outperforming SBA in accuracy and cross-chromophore consistency. While correlational-SBA offers a computationally efficient alternative and outperforms GLM-based methods, ICA should be preferred when reliable and chromophore-consistent RSFC estimates are required. Importantly, these findings demonstrate that HbR contains RSFC information comparable to HbO and highlights the critical role of analytical strategy and reference definition in RSFC evaluation. Collectively, these results contribute to the methodological standardization of fNIRS-based RSFC and support its use in future neuroscientific and clinical applications.