Mokotjo was handed the armband for the first time by coach Dean Smith for The Bees' fifth round Championship tie away to Blackburn Rovers on Saturday.
Despite dominating statistically, unfortunately the result didn't go his side's way as the hosts managed to steal all three points with a lone goal in the second half.
The skipper was critical of his charges' display as they suffered their first defeat of the season at Ewood Park, and felt their overall performance was below par.
"It was a very frustrating game from our side. We came up against a very organised, hard-working team but I felt we didn't give enough," Mokotjo told his club's website.
"That was just not our level. I think we didn't have to lose but you get what you deserve and at the end of the day ... But it's just one game, and we have to move on from this."
Brentford have this season established a rotation policy with the captaincy, which saw Mokotjo take on the responsibility this past weekend.
"I think [the rotation] is what the majority agreed on, and if that's the case then you take full responsibility when given the captain's armband," added the 27-year-old.
"For me it doesn't really change much because I know that every player in this team is responsible for themselves, so it just gives you a little boost but it doesn't change much."
After scoring his first goal of the season in the Carabao Cup last weekend, Mokotjo will be looking to build on his performance against fourth division side Cheltanham Town on Tuesday evening.