Growth pattern and condition factor (CF) are essential to fish resource assessment but limited to Periophthalmus gracilis—an amphibious fish living in the mudflats along the Indo-Pacific regions, including the Mekong Delta (MD), Vietnam. This study lasted from April 2020 to March 2021 to verify if their growth pattern and CF change with sex, size, season, month and site. The total length and weight of 486 individuals (236 females and 250 males) were 2.9–5.9 cm and 0.13–1.66 g, respectively. The mudskipper displayed negative allometry as the slope value (b = 2.69 ± 0.06) obtained from length and weight (LWR) was significantly less than 3 (p < 0.01), indicating that most fish specimens were caught in the immature stage. The fish growth pattern did not change with sex as both males and females displayed negative allometry but varied by size since the mudskipper showed negative allometry in the immature group and isometry in the mature group. Likewise, growth type changed with season since fish showed negative allometry in the dry season but isometry in the wet season. As the slope value (b) varied by site and month, the mudskipper displayed spatiotemporal growth patterns, ranging from negative to positive allometry. The CF was impacted by sex as this value of females (1.09 ± 0.02) was higher than that of males (0.96 ± 0.01, p < 0.01). Besides, CF was regulated by fish length since this value was higher in the mature group (1.12 ± 0.03) than in the immature group (1.01 ± 0.01, p < 0.01). Likewise, CF was affected by season as this value was higher in the wet season (1.05 ± 0.02) than in the dry season (0.99 ± 0.01, p < 0.01). Although the CF varied with site and month variables (p < 0.01), this value (1.02 ± 0.01) was generally higher than 1, showing fish adapted well to their habitat. The fish length at first capture should be increased to exploit this species sustainably.