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Young people exhibit a negative BOLD response in ipsilateral primary motor cortex (M1) when making unilateral movements, such as button presses. This negative BOLD response becomes more positive as people age. In this study, we investigated why this occurs, in terms of the underlying effective connectivity and haemodynamics. We applied dynamic causal modeling (DCM) to task fMRI data from 635 participants aged 18–88 from the Cam-CAN dataset, who performed a cued button pressing task with their right hand. We found that connectivity from contralateral supplementary motor area (SMA) and dorsal premotor cortex (PMd) to ipsilateral M1 became more positive with age, explaining 44% of the variability across people in ipsilateral M1 responses. In contrast, connectivity from contralateral M1 to ipsilateral M1 was weaker and did not correlate with individual differences in rM1 BOLD. Neurovascular and haemodynamic parameters in the model were not able to explain the age-related shift to positive BOLD. Our results add to a body of evidence implicating neural, rather than vascular factors as the predominant cause of negative BOLD—while emphasising the importance of inter-hemispheric connectivity. This study provides a foundation for investigating the clinical and lifestyle factors that determine the sign and amplitude of the M1 BOLD response in ageing, which could serve as a proxy for neural and vascular health, via the underlying neurovascular mechanisms.