"Science Fell in Love, So I Tried to Prove It" centers on two young scientists, Shinya Yukimura and Ayame Himuro, who work together in the same university laboratory. Both are highly logical and analytical, approaching life through the lens of scientific methodology. When Himuro confesses her feelings for Yukimura, he struggles to reconcile the concept of love with his empirical worldview. Rather than dismissing or accepting her confession outright, Yukimura proposes a scientific approach to determine whether their feelings for each other are genuine. The two embark on a series of experiments and observations to analyze love as a quantifiable phenomenon, using methods such as measuring heart rates, tracking behavioral changes, and conducting surveys.

The narrative explores their evolving relationship as they navigate the challenges of applying scientific rigor to emotions. Their experiments often lead to humorous and awkward situations, particularly when their colleagues, including the laid-back Kosuke Inukai and the sharp-tongued Ena Ibuki, become involved. The series balances comedic moments with thoughtful reflections on the nature of love, blending scientific inquiry with the unpredictability of human emotions. As the experiments progress, Yukimura and Himuro begin to question whether love can truly be reduced to data, leading to moments of introspection and growth for both characters. The story ultimately examines the intersection of logic and emotion, highlighting the complexities of relationships in a lighthearted yet meaningful way.