The efficiency of the termite Macrotermes bellicosus at digesting lignocellulose is due to its gut bacterial symbionts. We report the metagenome-assembled genome sequence of Burkholderia cepacia UJ_SKK_1.2, reconstructed from metagenomes produced from Macrotermes bellicosus gut microbiota. The 7,460,271-bp genome obtained consists of 6,763 protein-coding sequences, with 6,719 functionally assigned genes and 59 RNA genes.