Boyden joined the MIT faculty in 2007, and continues to develop new optogenetic tools as well as other technologies for the manipulation and analysis of brain structure and activity.

His mother has a masters in biochemistry and conducted nicotine research, staying home to tend to Boyden and his sister.

In 1999, Boyden began a PhD in neurosciences at Stanford University under the supervision of Jennifer Raymond and Richard Tsien.

[5] Following his PhD, Boyden worked as a Helen Hay Whitney postdoctoral fellow in the departments of bioengineering, applied physics, and biology at Stanford University for a year.

[5] Boyden's research encompasses optogenetics, expansion microscopy, deep brain stimulation, multiplexed imaging, machine learning, and more.

[9] Boyden reported in 2007 that targeting the codon-optimized light-driven halorhodopsin chloride pump (Halo) from Natronomas pharaonis allowed for optogenetic silencing with yellow light.

[12] This led to the first optogenetics in people in 2021, where a blind patient was injected with an adeno-associated viral vector encoding ChrimsonR coupled with goggle-enabled light stimulation.

[14] In 2017, Boyden designed a high-efficacy soma-targeted opsin through combining the N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the high-photocurrent channelrhodopsin CoChR.

[16] ExM has been optimized for proteins,[17] nucleic acids,[18] clinical tissues,[19] decrowding,[20] in situ sequencing,[21] and has developed a larger expansion factor.

By using hydrogel scaffolds, Implosion Fabrication (ImpFab) creates conductive 3D silver nanostructures with complex geometries and resolutions in the tens of nanometers.

[24] TI was validated in humans in 2023 where it modulated hippocampal activity and increased the accuracy of episodic memories in healthy subjects.

[30] Boyden has nearly 300 patented inventions, including a steerable surgical stapler, methods and apparatus for neuromodulation, expansion microscopy, and light-activated proton pumps.

[33] Elemind launched its neurotech headband that employs brainwaves to treat sleep disorders, long-term pain, and tremors on June 4, 2024.

Specifically, Boyden aims utilize findings about sensory stimulation evoking gamma activity in Alzheimer's disease to slow its progression.

[35] Boyden co-founded Expansion Technologies, aiming to enable the early disease detection by utilizing their novel super-resolution imaging method that physically expands samples,[36] as well as Synlife, which innovates therapeutic platforms through bottom-up engineering of synthetic cells with a focus on the encapsulation of enzyme pathways.

[38] He is the head of advisory board at Inner Cosmos whose mission is to heal depression with their Digital Pill, a penny-sized implant rebalancing brain networks with microstimulations.