Lukinavičius completed his bachelors degree and masters degree in biochemistry at the Vilnius University in 2000 and 2002 respectively. During this period he  worked as a research assistant in  Saulius Klimašauskas group and investigating conformational movements of the catalytic loop of DNA methyltransferase.
Later he became interested in S-Adenosyl methionine analogues which can be cofactors for methyltransferases. He collaborated with Elmar Weinhold from RWTH Aachen University and learned chemical synthesis and received his PhD in biochemistry at Vilnius University, Lithuania in September 2007. This led to the development of a new DNA labeling method, the Methyltransferase-Directed Transfer of Activated Groups (mTAG). This method was applied for optical DNA mapping and for a profiling epigenetic modifications by several research groups.
After obtaining his PhD, he moved to École polytechnique fédérale de Lausanne for postdoctoral research where he continued on working with protein labeling methods in group of Kai Johnsson. He improved SNAP-tag protein labelling technology by developing a new biocompatible fluorophore, silicon-rhodamine (SiR). During this period, he began a collaboration with Stefan Hell to perform one of the first super-resolution microscopy experiments of living cells.
In 2016, Stefan Hell invited Lukinavičius to the Department of NanoBiophotonics of the Max Planck Institute for Biophysical Chemistry in Göttingen. He has continued working on fluorescence labeling of biomolecules and started a Chromatin Labeling and Imaging group in 2018.