In the present work, optimum conditions for hydrocracking of waste palm cooking oil (WPCO) over a Ni-NH2/Lapindo mud catalyst were studied to obtain a high quantity and quality of biofuel. The utilized catalyst support material was Lapindo mud (LM) from Sidoarjo, Indonesia, which was only given physical treatment (i.e., washing, drying, grinding, and calcining). Ni/LM was prepared via wet impregnation in three different Ni weight loadings: 1, 5, and 10 wt.%, which were denoted as Ni(A)/LM, Ni(B)/LM, and Ni(C)/LM, respectively. As a result, the hydrocracking test of WPCO under the temperature of 470 °C and a feed/catalyst weight ratio of 50 showed that the Ni(A)/LM catalyst produced the highest liquid product reaching 46.65 wt.% among the other Ni-based catalysts. The liquid product can be increased drastically to 63.93 wt.% under a more optimum temperature at 550 °C. Functionalization of Ni(A)/LM as the best catalyst was carried out by grafting method with NH2 groups from 3-APTMS, resulting in Ni(A)-NH2/LM. This modification increased the liquid product to 68.17 wt.% under hydrocracking conditions using a weight ratio of 75. Moreover, the reusability of Ni(A)-NH2/LM was found to be effective for three hydrocracking runs, constantly yielding an average biofuel of 80 wt.%.