Supplemental lighting can enhance yield when sunlight is limited, as in winter. As the effect of frequent cloudy or rainy days in other seasons on plant growth and yield remains unclear, we investigated the effect on tomato (Solanum lycopersicum) and compensation by supplemental LED inter-lighting. Plants were grown under 30% shade cloth on 0%, 40%, or 60% of days. Lower leaves were illuminated with red and blue LED inter-lighting modules from right after first anthesis, or not illuminated. Shading during 40% and 60% of days diminished daily light integral (DLI) by 26% and 40%, respectively, and reduced shoot dry weight by 22.0% and 23.3%, yield by 18.5% and 23.3%, and fruit soluble solids content by 12.3% and 9.3%. In contrast, supplemental inter-lighting improved the light distribution within plants and compensated DLI, and maintained similar yield and soluble solids content in both shade treatments as in the control. These results clearly show that supplemental LED inter-lighting could efficiently compensate for a shortage of light for plant growth, photosynthesis and thus yield under the lack of sunshine.