The cranial window preparation provides optical access to the rodent brain for high-resolution in vivo optical imaging. Two types of cranial windows are commonly employed, namely the open-skull window and thinned-skull window. Chronic in vivo laser speckle contrast imaging (LSCI) through the cranial window permits characterization of neurovascular morphology and blood flow changes over days or weeks. However, the effects of window type and their long-term stability for in vivo LSCI have not been studied. Here we systematically characterize the effect of each cranial window type on in vivo neurovascular monitoring with LSCI over two weeks. Imaging outcomes for each window were assessed in terms of contrast-to-noise ratio (CNR), microvessel density (MVD) and total vessel length (TVL). We found that the thinned-skull window required a shorter recovery period (∼ 4 days), provided a larger field of view and was a good choice for short-term (i.e. < 10 days) in vivo imaging, but not for the long term because of the confounding effects of skull regrowth after ten days. The open-skull window required a longer recovery period, as made evident by the decrease in window quality within the 10-day period. In spite of this, the open-skull window would be preferable for chronic (i.e. < 10 days) in vivo imaging applications. Overall, this study informs about the pros and cons of each cranial window type for LSCI-based neurovascular imaging.