Microfluidic devices and lab-on-a-chip technologies have been extensively used in high-throughput single-cell analysis applications using their capability to precisely manipulate cells as well as their microenvironment. Although significant technological advances have been made in single-cell capture, culture, and analysis techniques, most microfluidic systems cannot selectively retrieve samples off-chip for additional examinations. Being able to retrieve target cells of interest from large arrays of single-cell culture compartments is especially critical in achieving high-throughput single-cell screening applications, such as a mutant library screening. We present a high-throughput microfluidic single-cell screening platform capable of investigating cell properties, such as growth and biomolecule production, followed by selective extraction of particular cells showing desired traits to off-chip reservoirs for sampling or further analysis. The developed platform consists of 1024 single-cell trapping/culturing sites, where opening and closing of each trap can be individually controlled with a microfluidic OR logic gate. By opening only a specific site out of the 1024 trapping sites and applying backflow, particular cells of interest could be selectively released and collected off-chip. Using a unicellular microalga Chlamydomonas reinhardtii, single-cell capture and selective cell extraction capabilities of the developed platform were successfully demonstrated. The growth profile and intracellular lipid accumulation of the cells were also analyzed inside the platform, where 6–8 hours of doubling time and on-chip stained lipid bodies were successfully identified, demonstrating the compatibility of the system for cell culture and fluorescent tagging assays.