Sugar beet (Beta vulgaris L. subsp. vulgaris) is deemed to be one of the most promising bioethanol feedstock crops in northern Japan. To establish viable sugar beet-based bioethanol production systems, energy-efficient protocols in sugar beet cultivation are being intensively sought. On this basis, the effects of alternative agronomic practices for sugar beet production on total energy inputs (from fuels and agricultural materials during cultivation and transportation) and ethanol yields (estimated from sugar yields) were assessed in terms of (i) direct drilling, (ii) reduced tillage (no moldboard plowing), (iii) no-fungicide application, (iv) using a high-yielding beet genotype, (v) delayed harvesting and (vi) root+crown harvesting. Compared with the conventional sugar beet production system used in the Tokachi region of Hokkaido, northern Japan, which makes use of transplants, direct drilling and no-fungicide application contributed to reduced energy inputs from raising seedlings and fungicides, respectively, but sugar (or ethanol) yields were also reduced by these practices, to a greater equivalent extent than the reductions in energy inputs. Consequently, direct drilling (6.84 MJ L−1) and no-fungicide application (7.78 MJ L−1) worsened the energy efficiency (total energy inputs to produce 1 L of ethanol), compared with conventional sugar beet production practices (5.82 MJ L−1). Sugar yields under conventional plow-based tillage and reduced tillage practices were similar, but total energy inputs were reduced as a result of reduced fuel consumption from not plowing. Hence, reduced tillage showed improved energy efficiency (5.36 MJ L−1). The energy efficiency was also improved by using a high-yielding genotype (5.23 MJ L−1) and root+crown harvesting (5.21 MJ L−1). For these practices, no major changes in total energy inputs were noted, but sugar yields were consistently increased. Neither total energy inputs nor ethanol yields were affected by extending the vegetative growing period by delaying harvesting.