Near-infrared optogenetics based on up-conversion materials provides a promising tool for the dissection of neural circuit functions in deep brain regions. However, it remains a challenge to combine near-infrared up-conversion optogenetic stimulation with high-density electrophysiological recording in a minimally invasive manner. Here, we develop a flexible device for simultaneous electrophysiological recording and near-infrared optogenetics. The flexible device is constructed by integrating polymer-based flexible recording microelectrodes with electrodeposited NaYF4:Yb3+, Er3+ up-conversion films that can convert deep-tissue-penetrating near-infrared light into visible light for optogenetic activation of C1V1-expressing neurons. The emission properties of the up-conversion films are optimized for green light emission to stimulate C1V1 opsins. Owing to their minimized surgical footprint and high mechanical compliance, chronically implanted devices enable simultaneous electrophysiological recording and near-infrared optogenetic modulation of neuronal activities in the brain.