This study aimed to develop a novel tomato (Solanum lycopersicum L.) cultivar enriched in phytoene and phytofluene, colorless carotenoids known for their health-promoting properties. Parental lines with diverse fruit colors and morphological traits were selected and crossbred to generate three F₁ hybrids: ‘Rubybell’, ‘INDIGO-G’, and ‘BLACK-B’. The phytoene and phytofluene contents of the hybrids were quantified using high-performance liquid chromatography. Among them, ‘Rubybell’ exhibited the highest concentrations of phytoene (0.105 mg/g) and total phytofluene (0.118 mg/g), representing increases of 51% and 29% compared to the maternal line APR-52-MU, and 14% and 1% compared to the paternal line CAPP1745, respectively. Compared to commercial tomato cultivars, ‘Rubybell’ exhibited 76- and 23-fold higher levels of phytoene and phytofluene, respectively. Furthermore, ‘Rubybell’ accumulated higher levels of these functional compounds when cultivated in March and October, underscoring the influence of the planting season on carotenoid biosynthesis. These findings offer valuable insights into the breeding of high-value functional tomatoes and support their potential use in health-promoting food applications (Registration number: 10514).