Rice eel (Monopterus albus) was introduced in the Philippines in 1905 as an aquaculture species without a thorough evaluation of its possible negative impact on the environment. In Cagayan Valley Region, it is being considered as a pest due to the economic loss it brought to farmers as it bore holes on the dikes, draining the water from the rice field, thus, contributing to the additional expense of the farmers. However, from the economic point of view, the species offered great potential as an export commodity due to its broad export market in East Asian countries. Hence, this study was conducted to determine the most efficient and effective method of controlling the proliferation of rice eel in rice fields in the Cagayan Valley region while preserving its integrity as an export commodity. Twelve (12) municipalities were chosen as the study sites based on validated reports of the high occurrence of rice eel. Three fishing methods, namely, fish trap (FT), hook and line (HL), and electrofishing (EF) gadget, were utilized. These gears were set during the dry and wet seasons. Catch and catch per unit effort (CPUE) were used to determine gear efficiency, while monetary values, net income, and ROI were used to assess the profitability of the gears. Results showed that electrofishing gadgets exhibit greater efficiency among the three fishing gears. The EF gadget also has the highest CPUE (4 individuals) per hour while only around 0–1 per hour for FT and HL. Seasonality does not affect the efficiency of the three fishing gears. Also, there is no significant interaction between seasons and fishing gears (p = 0.525). Computed annual net income and return on investment (ROI) is also greater using EF (PHP 407,630.40/ha/year with 569% ROI) compared to HL and FT (net incomes of PHP 113,244.68/ha/year and PHP 161,618.99/ha/year, and 261% and 309% ROI, respectively). However, the use of EF as a control measure should entail restrictions such that only within rice farm areas and not in open waters and only after harvest or before planting with issued EF licenses and permits from BFAR and local ordinances. Higher penalties should also be imposed for illegal use of EF such as use in open waters. As an alternative to EF, a combination of FT and HL with modifications or more environment-friendly fishing gears can be explored to catch and control the rice eel population.