As long as your file is actually "multi-fasta" and the sequence you want to remove is first one in the file, the following will work:

 awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < multifasta.fa | awk 'NR>1' | tr "\t" "\n"  > new.fa

Explanation: First awk command linearizes a multi-line multi-fasta file. Second awk command (after the pipe) removes the first line/record. Final tr command reformats the single line file back to a multi-fasta file.

Replace multifasta.fa with your input file. Choose file name you want for output in place of new.fa.