Half of the world’s population—more than 3.5 billion people—depend on rice for more than 20% of their daily energy requirements. Rice productivity is under threat for several reasons, particularly the deficiency of micronutrients, such as boron (B). Most rice-based cropping systems, including rice–wheat, are facing B deficiency as they are often practiced on high pH and alkaline soils with low B contents, low soil organic matter, and inadequate use of B fertilizer, which restricts the availability, uptake, and deposition of B into grains. Farmers’ reluctance to fertilize rice fields with B—due to the lack of cost-effective B-enriched macronutrient fertilizers—further exacerbates B deficiency in rice-based cropping systems. Here we review that, (i) while rice can tolerate excess B, its deficiency induces nutritional disorders, limits rice productivity, impairs grain quality, and affects the long-term sustainability of rice production systems. (ii) As B dynamics in the soil varies between flooded and aerobic rice systems, different B deficiency management strategies are needed in rice-based cropping systems. (iii) Correct diagnosis of B deficiency/toxicity in rice; understanding its interaction with other nutrients including nitrogen, phosphorus, potassium, and calcium; and the availability and application of B fertilizers using effective methods will help to improve the sustainability and productivity of different rice production systems. (iv) Research on rice-based systems should focus on breeding approaches, including marker-assisted selection and wide hybridization (incorporation of desirable genes), and biotechnological strategies, such as next-generation DNA and RNA sequencing, and genetic transformations to develop rice genotypes with improved B contents and abilities to acquire B from the soil. (v) Different B application strategies—seed priming and foliar and/or soil application—should be included to improve the performance of rice, particularly when grown under aerobic conditions.